Starting phenix.real_space_refine on Wed Jun 18 06:39:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmc_41384/06_2025/8tmc_41384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmc_41384/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmc_41384/06_2025/8tmc_41384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmc_41384/06_2025/8tmc_41384.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmc_41384/06_2025/8tmc_41384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmc_41384/06_2025/8tmc_41384.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.05, per 1000 atoms: 0.61 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: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.93 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: 5.72 Time building geometry restraints manager: 4.99 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.430 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- 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 : 12.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP F 123 HIS 0.004 0.001 HIS E 94 PHE 0.024 0.002 PHE E 79 TYR 0.025 0.001 TYR E 181 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.12214 ( 1074) hydrogen bonds : angle 6.34439 ( 3090) SS BOND : bond 0.00077 ( 4) SS BOND : angle 1.53294 ( 8) covalent geometry : bond 0.00389 (18471) covalent geometry : angle 0.63334 (25051) *********************** 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 : 1.973 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: 0.2747 time to fit residues: 189.5126 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 : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 90 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN C 95 GLN C 134 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN H 80 ASN L 39 GLN G 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.172983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146671 restraints weight = 23987.949| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.24 r_work: 0.3423 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 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 = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18475 Z= 0.166 Angle : 0.605 14.162 25059 Z= 0.314 Chirality : 0.044 0.217 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.495 28.600 2446 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 1.09 % Allowed : 10.35 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2180 helix: 2.06 (0.16), residues: 950 sheet: 0.69 (0.25), residues: 446 loop : -1.46 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 123 HIS 0.005 0.001 HIS B 212 PHE 0.025 0.001 PHE B 79 TYR 0.019 0.001 TYR L 50 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 1074) hydrogen bonds : angle 4.87040 ( 3090) SS BOND : bond 0.00103 ( 4) SS BOND : angle 1.09623 ( 8) covalent geometry : bond 0.00379 (18471) covalent geometry : angle 0.60514 (25051) *********************** 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 445 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 423 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8372 (pt0) cc_final: 0.7943 (pt0) REVERT: A 180 ASP cc_start: 0.8173 (t0) cc_final: 0.7953 (t0) REVERT: A 189 ASP cc_start: 0.7290 (t0) cc_final: 0.6994 (t0) REVERT: A 230 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6292 (mm-30) REVERT: A 245 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7838 (mmtm) REVERT: A 276 LEU cc_start: 0.7566 (mt) cc_final: 0.7294 (mt) REVERT: A 334 MET cc_start: 0.6638 (mtp) cc_final: 0.6255 (mtp) REVERT: B 28 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 37 GLU cc_start: 0.7194 (pm20) cc_final: 0.6925 (pm20) REVERT: B 79 PHE cc_start: 0.7273 (t80) cc_final: 0.6954 (t80) REVERT: B 133 LYS cc_start: 0.7820 (tptp) cc_final: 0.7499 (tptp) REVERT: B 186 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6825 (mm-30) REVERT: B 192 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 230 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6968 (mt-10) REVERT: B 296 ILE cc_start: 0.8475 (mp) cc_final: 0.8222 (mp) REVERT: C 104 ASN cc_start: 0.8667 (m-40) cc_final: 0.8456 (m-40) REVERT: C 193 ASP cc_start: 0.8102 (t0) cc_final: 0.7836 (t0) REVERT: C 289 GLU cc_start: 0.7670 (tt0) cc_final: 0.7462 (tt0) REVERT: C 334 MET cc_start: 0.6563 (ttt) cc_final: 0.6172 (ttt) REVERT: D 291 MET cc_start: 0.8436 (tpp) cc_final: 0.8065 (tpp) REVERT: D 313 MET cc_start: 0.5021 (mtt) cc_final: 0.4652 (mpp) REVERT: E 37 GLU cc_start: 0.7760 (pp20) cc_final: 0.7271 (pp20) REVERT: H 9 GLU cc_start: 0.6639 (mp0) cc_final: 0.6195 (mp0) REVERT: H 93 ASP cc_start: 0.8525 (m-30) cc_final: 0.8222 (m-30) REVERT: L 80 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7698 (mm-40) REVERT: F 70 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7085 (ptt180) outliers start: 22 outliers final: 15 residues processed: 431 average time/residue: 0.2767 time to fit residues: 186.4733 Evaluate side-chains 411 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 395 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 27 optimal weight: 1.9990 chunk 193 optimal weight: 0.0020 chunk 76 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS C 134 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.174499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148473 restraints weight = 23987.107| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.24 r_work: 0.3441 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18475 Z= 0.129 Angle : 0.565 11.523 25059 Z= 0.293 Chirality : 0.042 0.189 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.356 27.069 2446 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.54 % Allowed : 12.98 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2180 helix: 2.27 (0.17), residues: 950 sheet: 0.72 (0.25), residues: 436 loop : -1.45 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 123 HIS 0.005 0.001 HIS B 212 PHE 0.019 0.001 PHE H 71 TYR 0.021 0.001 TYR L 50 ARG 0.005 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1074) hydrogen bonds : angle 4.60240 ( 3090) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.74954 ( 8) covalent geometry : bond 0.00287 (18471) covalent geometry : angle 0.56533 (25051) *********************** 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 439 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 408 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8300 (pt0) cc_final: 0.7826 (pt0) REVERT: A 189 ASP cc_start: 0.7224 (t0) cc_final: 0.6885 (t0) REVERT: A 230 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6263 (mm-30) REVERT: A 245 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7820 (mmtm) REVERT: B 78 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: B 79 PHE cc_start: 0.7269 (t80) cc_final: 0.7031 (t80) REVERT: B 133 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7417 (tptp) REVERT: B 186 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6788 (mm-30) REVERT: B 192 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 260 GLN cc_start: 0.7203 (tt0) cc_final: 0.6962 (tt0) REVERT: B 296 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 162 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: C 193 ASP cc_start: 0.8046 (t0) cc_final: 0.7797 (t0) REVERT: C 289 GLU cc_start: 0.7564 (tt0) cc_final: 0.7262 (tt0) REVERT: C 334 MET cc_start: 0.6772 (ttt) cc_final: 0.6433 (ttt) REVERT: D 232 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8346 (mm) REVERT: D 291 MET cc_start: 0.8445 (tpp) cc_final: 0.8016 (tpp) REVERT: E 37 GLU cc_start: 0.7849 (pp20) cc_final: 0.7223 (pp20) REVERT: E 112 MET cc_start: 0.8854 (mtp) cc_final: 0.8581 (mtm) REVERT: E 125 GLU cc_start: 0.8223 (tt0) cc_final: 0.7968 (tt0) REVERT: H 9 GLU cc_start: 0.6423 (mp0) cc_final: 0.6007 (mp0) REVERT: H 93 ASP cc_start: 0.8473 (m-30) cc_final: 0.7918 (m-30) REVERT: L 80 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7871 (mm-40) REVERT: F 70 ARG cc_start: 0.7904 (mtm110) cc_final: 0.6951 (ptt180) outliers start: 31 outliers final: 17 residues processed: 420 average time/residue: 0.2797 time to fit residues: 183.8174 Evaluate side-chains 410 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 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 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 127 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 134 ASN H 80 ASN L 39 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.170048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.143645 restraints weight = 24212.744| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.24 r_work: 0.3386 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18475 Z= 0.202 Angle : 0.608 9.736 25059 Z= 0.312 Chirality : 0.044 0.230 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.465 26.484 2446 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 2.72 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2180 helix: 2.12 (0.17), residues: 955 sheet: 0.64 (0.25), residues: 446 loop : -1.57 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 123 HIS 0.007 0.001 HIS B 212 PHE 0.016 0.002 PHE C 306 TYR 0.022 0.001 TYR L 50 ARG 0.003 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 1074) hydrogen bonds : angle 4.66910 ( 3090) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.94007 ( 8) covalent geometry : bond 0.00480 (18471) covalent geometry : angle 0.60781 (25051) *********************** 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 466 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 411 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7557 (t0) cc_final: 0.7040 (m-30) REVERT: A 30 GLU cc_start: 0.8275 (pt0) cc_final: 0.7773 (pt0) REVERT: A 189 ASP cc_start: 0.7327 (t0) cc_final: 0.6963 (t0) REVERT: A 230 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6499 (mm-30) REVERT: A 245 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7774 (mmtm) REVERT: A 276 LEU cc_start: 0.7647 (mt) cc_final: 0.7350 (mt) REVERT: B 37 GLU cc_start: 0.7127 (pm20) cc_final: 0.6878 (pm20) REVERT: B 78 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: B 133 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7442 (tptp) REVERT: B 138 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8238 (ttp) REVERT: B 186 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 192 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8582 (mp) REVERT: B 193 ASP cc_start: 0.7930 (t0) cc_final: 0.7579 (t0) REVERT: B 296 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 306 PHE cc_start: 0.7289 (t80) cc_final: 0.6914 (t80) REVERT: C 193 ASP cc_start: 0.8085 (t0) cc_final: 0.7823 (t0) REVERT: C 289 GLU cc_start: 0.7645 (tt0) cc_final: 0.7356 (tt0) REVERT: D 232 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 70 THR cc_start: 0.8138 (p) cc_final: 0.7858 (m) REVERT: E 112 MET cc_start: 0.8915 (mtp) cc_final: 0.8681 (mtm) REVERT: E 125 GLU cc_start: 0.8263 (tt0) cc_final: 0.7980 (tt0) REVERT: H 38 HIS cc_start: 0.8412 (m170) cc_final: 0.7981 (m90) REVERT: H 93 ASP cc_start: 0.8491 (m-30) cc_final: 0.7981 (m-30) REVERT: H 120 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: L 80 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7862 (mm-40) REVERT: F 70 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7009 (ptt180) outliers start: 55 outliers final: 35 residues processed: 434 average time/residue: 0.2805 time to fit residues: 187.7946 Evaluate side-chains 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 405 time to evaluate : 2.022 ------------------------------------------------------------------------------- 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 A residue 283 VAL 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 138 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 272 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 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 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 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 39 GLN 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 157 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 103 optimal weight: 0.0270 chunk 137 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 109 optimal weight: 0.1980 chunk 204 optimal weight: 0.0570 chunk 177 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 104 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.173207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147059 restraints weight = 24293.101| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.25 r_work: 0.3428 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18475 Z= 0.126 Angle : 0.558 8.287 25059 Z= 0.289 Chirality : 0.042 0.169 2823 Planarity : 0.004 0.051 3137 Dihedral : 4.335 25.652 2446 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 2.58 % Allowed : 15.90 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2180 helix: 2.28 (0.17), residues: 956 sheet: 0.73 (0.25), residues: 435 loop : -1.48 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 50 HIS 0.007 0.001 HIS C 83 PHE 0.016 0.001 PHE G 63 TYR 0.018 0.001 TYR L 50 ARG 0.005 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1074) hydrogen bonds : angle 4.51567 ( 3090) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.68146 ( 8) covalent geometry : bond 0.00284 (18471) covalent geometry : angle 0.55843 (25051) *********************** 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 450 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 398 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8243 (pt0) cc_final: 0.7680 (pt0) REVERT: A 189 ASP cc_start: 0.7272 (t0) cc_final: 0.6973 (t0) REVERT: A 205 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7421 (mtpp) REVERT: A 230 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6430 (mm-30) REVERT: A 276 LEU cc_start: 0.7591 (mt) cc_final: 0.7287 (mt) REVERT: B 79 PHE cc_start: 0.7315 (t80) cc_final: 0.6894 (t80) REVERT: B 133 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7434 (tptp) REVERT: B 186 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 192 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 193 ASP cc_start: 0.7865 (t0) cc_final: 0.7511 (t0) REVERT: B 260 GLN cc_start: 0.7158 (tt0) cc_final: 0.6934 (tt0) REVERT: B 296 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 306 PHE cc_start: 0.7397 (t80) cc_final: 0.7036 (t80) REVERT: C 193 ASP cc_start: 0.8075 (t0) cc_final: 0.7802 (t0) REVERT: C 289 GLU cc_start: 0.7671 (tt0) cc_final: 0.7355 (tt0) REVERT: D 226 TRP cc_start: 0.8293 (m100) cc_final: 0.7835 (m100) REVERT: D 232 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8357 (mm) REVERT: D 313 MET cc_start: 0.4943 (mtt) cc_final: 0.4555 (mpp) REVERT: E 37 GLU cc_start: 0.7897 (pp20) cc_final: 0.7597 (pp20) REVERT: E 232 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8392 (mm) REVERT: H 9 GLU cc_start: 0.6286 (mp0) cc_final: 0.5760 (mp0) REVERT: H 38 HIS cc_start: 0.8365 (m170) cc_final: 0.8049 (m90) REVERT: H 93 ASP cc_start: 0.8457 (m-30) cc_final: 0.7995 (m-30) REVERT: L 80 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7897 (mm-40) REVERT: F 70 ARG cc_start: 0.7844 (mtm110) cc_final: 0.7045 (ptt180) outliers start: 52 outliers final: 34 residues processed: 425 average time/residue: 0.2754 time to fit residues: 182.9566 Evaluate side-chains 422 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 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 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 253 ASP 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 134 ASN 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 341 MET Chi-restraints excluded: chain H residue 65 ASP 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 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.172100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.145688 restraints weight = 24367.808| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.26 r_work: 0.3406 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18475 Z= 0.156 Angle : 0.574 8.961 25059 Z= 0.296 Chirality : 0.043 0.279 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.348 25.243 2446 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 2.92 % Allowed : 17.19 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2180 helix: 2.27 (0.17), residues: 958 sheet: 0.74 (0.25), residues: 433 loop : -1.48 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 50 HIS 0.006 0.001 HIS B 212 PHE 0.022 0.001 PHE C 306 TYR 0.017 0.001 TYR L 50 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1074) hydrogen bonds : angle 4.53156 ( 3090) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.77668 ( 8) covalent geometry : bond 0.00365 (18471) covalent geometry : angle 0.57432 (25051) *********************** 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 449 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 2.188 Fit side-chains revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8292 (t80) cc_final: 0.8072 (t80) REVERT: A 30 GLU cc_start: 0.8249 (pt0) cc_final: 0.7719 (pt0) REVERT: A 189 ASP cc_start: 0.7316 (t0) cc_final: 0.7000 (t0) REVERT: A 205 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7477 (mtpp) REVERT: A 230 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6480 (mm-30) REVERT: A 232 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 276 LEU cc_start: 0.7630 (mt) cc_final: 0.7310 (mt) REVERT: B 79 PHE cc_start: 0.7326 (t80) cc_final: 0.6933 (t80) REVERT: B 133 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7438 (tptp) REVERT: B 186 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6956 (mm-30) REVERT: B 192 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 193 ASP cc_start: 0.7870 (t0) cc_final: 0.7523 (t0) REVERT: B 230 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 260 GLN cc_start: 0.7151 (tt0) cc_final: 0.6928 (tt0) REVERT: B 296 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8372 (mp) REVERT: B 306 PHE cc_start: 0.7446 (t80) cc_final: 0.7079 (t80) REVERT: B 346 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7896 (mmmt) REVERT: C 193 ASP cc_start: 0.8086 (t0) cc_final: 0.7807 (t0) REVERT: C 289 GLU cc_start: 0.7719 (tt0) cc_final: 0.7375 (tt0) REVERT: D 232 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8376 (mm) REVERT: D 291 MET cc_start: 0.8517 (tpp) cc_final: 0.8236 (tpp) REVERT: E 37 GLU cc_start: 0.7919 (pp20) cc_final: 0.7600 (pp20) REVERT: E 70 THR cc_start: 0.8099 (p) cc_final: 0.7810 (m) REVERT: E 112 MET cc_start: 0.9014 (mtp) cc_final: 0.8699 (mtm) REVERT: E 232 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (mm) REVERT: H 9 GLU cc_start: 0.6356 (mp0) cc_final: 0.5778 (mp0) REVERT: H 38 HIS cc_start: 0.8369 (m170) cc_final: 0.7954 (m90) REVERT: H 93 ASP cc_start: 0.8459 (m-30) cc_final: 0.7988 (m-30) REVERT: H 120 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7853 (mtm) REVERT: L 80 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7957 (mm-40) REVERT: F 70 ARG cc_start: 0.7861 (mtm110) cc_final: 0.6880 (ptt180) outliers start: 59 outliers final: 41 residues processed: 419 average time/residue: 0.2801 time to fit residues: 184.8685 Evaluate side-chains 428 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 380 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 B residue 18 VAL Chi-restraints excluded: chain B residue 37 GLU 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 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 253 ASP 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 318 MET Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 56 SER 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 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 341 MET Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 12 LEU 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 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 154 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.172708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146455 restraints weight = 24194.699| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.24 r_work: 0.3411 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18475 Z= 0.144 Angle : 0.566 8.873 25059 Z= 0.291 Chirality : 0.042 0.176 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.325 24.621 2446 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.72 % Allowed : 17.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2180 helix: 2.30 (0.16), residues: 958 sheet: 0.73 (0.25), residues: 433 loop : -1.50 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.022 0.001 PHE C 306 TYR 0.017 0.001 TYR L 56 ARG 0.005 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 1074) hydrogen bonds : angle 4.48633 ( 3090) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.75937 ( 8) covalent geometry : bond 0.00334 (18471) covalent geometry : angle 0.56584 (25051) *********************** 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 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 392 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8282 (pt0) cc_final: 0.7703 (pt0) REVERT: A 189 ASP cc_start: 0.7267 (t0) cc_final: 0.6978 (t0) REVERT: A 205 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7450 (mtpp) REVERT: A 230 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6462 (mm-30) REVERT: A 232 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 276 LEU cc_start: 0.7603 (mt) cc_final: 0.7331 (mt) REVERT: B 10 LYS cc_start: 0.7016 (mtpp) cc_final: 0.6780 (mtpt) REVERT: B 79 PHE cc_start: 0.7346 (t80) cc_final: 0.6996 (t80) REVERT: B 133 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7397 (tptp) REVERT: B 186 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 192 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 193 ASP cc_start: 0.7869 (t0) cc_final: 0.7522 (t0) REVERT: B 230 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7023 (mt-10) REVERT: B 296 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 193 ASP cc_start: 0.8076 (t0) cc_final: 0.7795 (t0) REVERT: D 226 TRP cc_start: 0.8319 (m100) cc_final: 0.7867 (m100) REVERT: D 232 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8356 (mm) REVERT: E 70 THR cc_start: 0.8138 (p) cc_final: 0.7822 (m) REVERT: E 112 MET cc_start: 0.9021 (mtp) cc_final: 0.8706 (mtm) REVERT: E 232 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8382 (mm) REVERT: H 38 HIS cc_start: 0.8346 (m170) cc_final: 0.7885 (m90) REVERT: H 93 ASP cc_start: 0.8453 (m-30) cc_final: 0.7978 (m-30) REVERT: H 120 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7748 (mtm) REVERT: L 80 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7953 (mm-40) REVERT: F 70 ARG cc_start: 0.7901 (mtm110) cc_final: 0.6955 (ptt180) outliers start: 55 outliers final: 41 residues processed: 426 average time/residue: 0.2747 time to fit residues: 183.3884 Evaluate side-chains 422 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 37 GLU Chi-restraints excluded: chain B residue 47 VAL 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 253 ASP 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 232 LEU Chi-restraints excluded: chain D residue 265 VAL 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 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 91 GLN 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 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 3 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 314 ASN H 80 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.168867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142286 restraints weight = 24158.870| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.23 r_work: 0.3369 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18475 Z= 0.222 Angle : 0.627 10.991 25059 Z= 0.322 Chirality : 0.044 0.224 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.501 24.681 2446 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 3.27 % Allowed : 18.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2180 helix: 2.10 (0.16), residues: 958 sheet: 0.49 (0.25), residues: 430 loop : -1.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.024 0.002 PHE C 306 TYR 0.018 0.002 TYR C 236 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 1074) hydrogen bonds : angle 4.65225 ( 3090) SS BOND : bond 0.00350 ( 4) SS BOND : angle 0.88336 ( 8) covalent geometry : bond 0.00529 (18471) covalent geometry : angle 0.62673 (25051) *********************** 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 454 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 388 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8306 (pt0) cc_final: 0.7759 (pt0) REVERT: A 189 ASP cc_start: 0.7267 (t0) cc_final: 0.6976 (t0) REVERT: A 230 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 232 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 276 LEU cc_start: 0.7656 (mt) cc_final: 0.7373 (mt) REVERT: B 10 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6918 (mtpt) REVERT: B 133 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7386 (tptp) REVERT: B 186 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7088 (mm-30) REVERT: B 192 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 193 ASP cc_start: 0.7958 (t0) cc_final: 0.7582 (t0) REVERT: B 260 GLN cc_start: 0.7208 (tt0) cc_final: 0.6990 (tt0) REVERT: B 292 LYS cc_start: 0.7603 (mttp) cc_final: 0.7208 (tttp) REVERT: B 296 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8453 (mp) REVERT: C 193 ASP cc_start: 0.8113 (t0) cc_final: 0.7833 (t0) REVERT: D 232 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8423 (mm) REVERT: E 162 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8132 (tpt90) REVERT: E 232 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8483 (mm) REVERT: H 38 HIS cc_start: 0.8439 (m170) cc_final: 0.7974 (m90) REVERT: H 93 ASP cc_start: 0.8452 (m-30) cc_final: 0.8003 (m-30) REVERT: H 120 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7910 (mtm) REVERT: L 80 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7947 (mm-40) REVERT: F 70 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7021 (ptt180) outliers start: 66 outliers final: 46 residues processed: 424 average time/residue: 0.2895 time to fit residues: 190.5632 Evaluate side-chains 432 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 378 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 37 GLU 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 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 134 ASN 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 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 162 ARG Chi-restraints excluded: chain E residue 170 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 314 ASN Chi-restraints excluded: chain E residue 329 VAL 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 12 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 285 ASN E 314 ASN H 80 ASN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.171774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144988 restraints weight = 24115.032| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.35 r_work: 0.3372 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1801 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= 0.177 Angle : 0.611 10.431 25059 Z= 0.314 Chirality : 0.044 0.230 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.477 24.497 2446 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.82 % Allowed : 18.87 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2180 helix: 2.16 (0.16), residues: 956 sheet: 0.47 (0.25), residues: 429 loop : -1.53 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.025 0.002 PHE C 306 TYR 0.020 0.001 TYR L 56 ARG 0.007 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1074) hydrogen bonds : angle 4.62588 ( 3090) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.77894 ( 8) covalent geometry : bond 0.00419 (18471) covalent geometry : angle 0.61064 (25051) *********************** 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 450 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8351 (pt0) cc_final: 0.7797 (pt0) REVERT: A 189 ASP cc_start: 0.7273 (t0) cc_final: 0.6989 (t0) REVERT: A 230 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6510 (mm-30) REVERT: A 232 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8294 (mm) REVERT: A 276 LEU cc_start: 0.7651 (mt) cc_final: 0.7350 (mt) REVERT: B 10 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6933 (mtpt) REVERT: B 133 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7372 (tptp) REVERT: B 186 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 192 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 193 ASP cc_start: 0.7979 (t0) cc_final: 0.7591 (t0) REVERT: B 260 GLN cc_start: 0.7132 (tt0) cc_final: 0.6925 (tt0) REVERT: B 292 LYS cc_start: 0.7502 (mttp) cc_final: 0.7120 (tttp) REVERT: B 296 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 193 ASP cc_start: 0.8132 (t0) cc_final: 0.7840 (t0) REVERT: C 289 GLU cc_start: 0.7787 (tt0) cc_final: 0.7403 (tt0) REVERT: C 301 PHE cc_start: 0.8238 (m-10) cc_final: 0.8003 (m-80) REVERT: D 226 TRP cc_start: 0.8267 (m100) cc_final: 0.7843 (m100) REVERT: D 232 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 162 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8115 (tpt90) REVERT: E 232 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8452 (mm) REVERT: H 38 HIS cc_start: 0.8442 (m170) cc_final: 0.7981 (m90) REVERT: H 93 ASP cc_start: 0.8437 (m-30) cc_final: 0.7988 (m-30) REVERT: H 120 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: L 80 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7988 (mm-40) REVERT: F 70 ARG cc_start: 0.7940 (mtm110) cc_final: 0.6956 (ptt180) outliers start: 57 outliers final: 45 residues processed: 424 average time/residue: 0.2756 time to fit residues: 181.8387 Evaluate side-chains 436 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 383 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 B residue 18 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 37 GLU 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 253 ASP 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 51 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 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 162 ARG Chi-restraints excluded: chain E residue 170 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 329 VAL 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 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 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN G 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.169945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.143458 restraints weight = 24171.846| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.23 r_work: 0.3379 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18475 Z= 0.189 Angle : 0.626 12.280 25059 Z= 0.320 Chirality : 0.044 0.217 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.520 24.458 2446 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer: Outliers : 2.77 % Allowed : 18.92 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2180 helix: 2.13 (0.16), residues: 956 sheet: 0.41 (0.25), residues: 443 loop : -1.59 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.026 0.002 PHE C 306 TYR 0.023 0.002 TYR B 255 ARG 0.006 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1074) hydrogen bonds : angle 4.65203 ( 3090) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.82517 ( 8) covalent geometry : bond 0.00451 (18471) covalent geometry : angle 0.62640 (25051) ********************** 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 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8347 (pt0) cc_final: 0.7818 (pt0) REVERT: A 189 ASP cc_start: 0.7337 (t0) cc_final: 0.7000 (t0) REVERT: A 230 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 232 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8321 (mm) REVERT: A 276 LEU cc_start: 0.7712 (mt) cc_final: 0.7352 (mt) REVERT: B 10 LYS cc_start: 0.7275 (mtpp) cc_final: 0.7030 (mtpt) REVERT: B 133 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7368 (tptp) REVERT: B 186 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 192 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 193 ASP cc_start: 0.7929 (t0) cc_final: 0.7591 (t0) REVERT: B 292 LYS cc_start: 0.7525 (mttp) cc_final: 0.7135 (tttp) REVERT: B 296 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 306 PHE cc_start: 0.7473 (t80) cc_final: 0.6998 (t80) REVERT: C 193 ASP cc_start: 0.8073 (t0) cc_final: 0.7788 (t0) REVERT: C 289 GLU cc_start: 0.7727 (tt0) cc_final: 0.7325 (tt0) REVERT: C 301 PHE cc_start: 0.8122 (m-10) cc_final: 0.7910 (m-80) REVERT: D 226 TRP cc_start: 0.8294 (m100) cc_final: 0.7897 (m100) REVERT: D 232 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 162 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8125 (tpt90) REVERT: E 232 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8431 (mm) REVERT: H 38 HIS cc_start: 0.8462 (m170) cc_final: 0.8000 (m90) REVERT: H 93 ASP cc_start: 0.8413 (m-30) cc_final: 0.7978 (m-30) REVERT: H 120 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: L 80 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8012 (mm-40) REVERT: F 70 ARG cc_start: 0.7900 (mtm110) cc_final: 0.6955 (ptt180) outliers start: 56 outliers final: 44 residues processed: 421 average time/residue: 0.2762 time to fit residues: 180.7888 Evaluate side-chains 438 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 386 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 B residue 18 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 37 GLU 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 253 ASP 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 51 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 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 162 ARG 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 329 VAL Chi-restraints excluded: chain E residue 341 MET 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 61 SER Chi-restraints excluded: chain L residue 91 GLN 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 174 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 205 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** H 80 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.171849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.145487 restraints weight = 24254.184| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.25 r_work: 0.3407 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18475 Z= 0.145 Angle : 0.609 16.422 25059 Z= 0.311 Chirality : 0.043 0.159 2823 Planarity : 0.005 0.051 3137 Dihedral : 4.425 24.017 2446 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.77 % Allowed : 19.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2180 helix: 2.26 (0.17), residues: 956 sheet: 0.58 (0.25), residues: 433 loop : -1.60 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.025 0.001 PHE C 306 TYR 0.019 0.001 TYR B 255 ARG 0.009 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1074) hydrogen bonds : angle 4.56567 ( 3090) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.73068 ( 8) covalent geometry : bond 0.00339 (18471) covalent geometry : angle 0.60943 (25051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9443.27 seconds wall clock time: 162 minutes 34.53 seconds (9754.53 seconds total)