Starting phenix.real_space_refine on Wed May 21 03:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmc_41384/05_2025/8tmc_41384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmc_41384/05_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_41384/05_2025/8tmc_41384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmc_41384/05_2025/8tmc_41384.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmc_41384/05_2025/8tmc_41384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmc_41384/05_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-5687/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: 10.93, 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: 4.59 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: 2.05 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: 5.26 Time building geometry restraints manager: 5.31 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.860 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.110 ------------------------------------------------------------------------------- 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 : 1.998 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: 0.2662 time to fit residues: 182.4465 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 : 1.868 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.173486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.147224 restraints weight = 23958.352| |-----------------------------------------------------------------------------| r_work (start): 0.3537 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: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 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 = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 1.887 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8370 (pt0) cc_final: 0.7941 (pt0) REVERT: A 180 ASP cc_start: 0.8178 (t0) cc_final: 0.7959 (t0) REVERT: A 189 ASP cc_start: 0.7289 (t0) cc_final: 0.6994 (t0) REVERT: A 230 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6296 (mm-30) REVERT: A 245 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7839 (mmtm) REVERT: A 276 LEU cc_start: 0.7568 (mt) cc_final: 0.7295 (mt) REVERT: A 334 MET cc_start: 0.6639 (mtp) cc_final: 0.6254 (mtp) REVERT: B 28 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 37 GLU cc_start: 0.7194 (pm20) cc_final: 0.6926 (pm20) REVERT: B 79 PHE cc_start: 0.7274 (t80) cc_final: 0.6954 (t80) REVERT: B 133 LYS cc_start: 0.7821 (tptp) cc_final: 0.7501 (tptp) REVERT: B 186 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 192 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 230 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 296 ILE cc_start: 0.8478 (mp) cc_final: 0.8225 (mp) REVERT: C 104 ASN cc_start: 0.8663 (m-40) cc_final: 0.8454 (m-40) REVERT: C 193 ASP cc_start: 0.8099 (t0) cc_final: 0.7832 (t0) REVERT: C 289 GLU cc_start: 0.7672 (tt0) cc_final: 0.7465 (tt0) REVERT: C 334 MET cc_start: 0.6568 (ttt) cc_final: 0.6177 (ttt) REVERT: D 291 MET cc_start: 0.8438 (tpp) cc_final: 0.8066 (tpp) REVERT: D 313 MET cc_start: 0.5020 (mtt) cc_final: 0.4653 (mpp) REVERT: E 37 GLU cc_start: 0.7756 (pp20) cc_final: 0.7269 (pp20) REVERT: H 9 GLU cc_start: 0.6644 (mp0) cc_final: 0.6202 (mp0) REVERT: H 93 ASP cc_start: 0.8526 (m-30) cc_final: 0.8225 (m-30) REVERT: L 80 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7702 (mm-40) REVERT: F 70 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7088 (ptt180) outliers start: 22 outliers final: 15 residues processed: 431 average time/residue: 0.2628 time to fit residues: 176.4224 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 : 1.881 ------------------------------------------------------------------------------- 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: 0.0470 chunk 76 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 152 optimal weight: 0.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.174378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.148361 restraints weight = 23985.182| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.24 r_work: 0.3443 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1174 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 : 0.566 11.502 25059 Z= 0.293 Chirality : 0.042 0.188 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.362 27.097 2446 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.58 % Allowed : 12.93 % 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: 0.99 (0.18), residues: 2180 helix: 2.27 (0.17), residues: 950 sheet: 0.71 (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 0.006 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 1074) hydrogen bonds : angle 4.60878 ( 3090) SS BOND : bond 0.00384 ( 4) SS BOND : angle 0.80339 ( 8) covalent geometry : bond 0.00288 (18471) covalent geometry : angle 0.56609 (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 441 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 409 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8296 (pt0) cc_final: 0.7824 (pt0) REVERT: A 189 ASP cc_start: 0.7220 (t0) cc_final: 0.6883 (t0) REVERT: A 230 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6256 (mm-30) REVERT: A 245 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7830 (mmtm) REVERT: B 78 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: B 79 PHE cc_start: 0.7272 (t80) cc_final: 0.7038 (t80) REVERT: B 133 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7419 (tptp) REVERT: B 186 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6796 (mm-30) REVERT: B 192 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 260 GLN cc_start: 0.7176 (tt0) cc_final: 0.6947 (tt0) REVERT: B 296 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 162 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8455 (mmm-85) REVERT: C 193 ASP cc_start: 0.8047 (t0) cc_final: 0.7797 (t0) REVERT: C 289 GLU cc_start: 0.7572 (tt0) cc_final: 0.7265 (tt0) REVERT: C 334 MET cc_start: 0.6747 (ttt) cc_final: 0.6402 (ttt) REVERT: D 232 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8345 (mm) REVERT: D 291 MET cc_start: 0.8448 (tpp) cc_final: 0.8009 (tpp) REVERT: E 37 GLU cc_start: 0.7847 (pp20) cc_final: 0.7221 (pp20) REVERT: E 112 MET cc_start: 0.8853 (mtp) cc_final: 0.8578 (mtm) REVERT: E 125 GLU cc_start: 0.8225 (tt0) cc_final: 0.7971 (tt0) REVERT: H 9 GLU cc_start: 0.6438 (mp0) cc_final: 0.6021 (mp0) REVERT: H 93 ASP cc_start: 0.8479 (m-30) cc_final: 0.7929 (m-30) REVERT: L 80 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7867 (mm-40) REVERT: F 70 ARG cc_start: 0.7904 (mtm110) cc_final: 0.6953 (ptt180) outliers start: 32 outliers final: 19 residues processed: 421 average time/residue: 0.2725 time to fit residues: 178.2846 Evaluate side-chains 418 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 394 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 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 L residue 39 GLN 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: 0.9980 chunk 146 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 90 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.172515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146258 restraints weight = 24175.209| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.25 r_work: 0.3408 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18475 Z= 0.165 Angle : 0.582 9.012 25059 Z= 0.299 Chirality : 0.043 0.249 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.378 26.270 2446 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 2.53 % Allowed : 14.41 % Favored : 83.06 % 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: 0.95 (0.18), residues: 2180 helix: 2.21 (0.17), residues: 952 sheet: 0.77 (0.25), residues: 433 loop : -1.50 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 123 HIS 0.006 0.001 HIS B 212 PHE 0.015 0.001 PHE C 306 TYR 0.022 0.001 TYR L 50 ARG 0.003 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 1074) hydrogen bonds : angle 4.58606 ( 3090) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.86618 ( 8) covalent geometry : bond 0.00389 (18471) covalent geometry : angle 0.58159 (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 452 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8214 (pt0) cc_final: 0.7696 (pt0) REVERT: A 143 ILE cc_start: 0.8577 (tp) cc_final: 0.8370 (mm) REVERT: A 189 ASP cc_start: 0.7302 (t0) cc_final: 0.6952 (t0) REVERT: A 230 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6431 (mm-30) REVERT: A 245 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7776 (mmtm) REVERT: A 276 LEU cc_start: 0.7609 (mt) cc_final: 0.7321 (mt) REVERT: B 37 GLU cc_start: 0.7095 (pm20) cc_final: 0.6844 (pm20) REVERT: B 78 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: B 133 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7432 (tptp) REVERT: B 165 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: B 186 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6884 (mm-30) REVERT: B 192 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 193 ASP cc_start: 0.7912 (t0) cc_final: 0.7558 (t0) REVERT: B 296 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8311 (mp) REVERT: C 193 ASP cc_start: 0.8074 (t0) cc_final: 0.7809 (t0) REVERT: C 289 GLU cc_start: 0.7632 (tt0) cc_final: 0.7372 (tt0) REVERT: D 232 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8375 (mm) REVERT: D 313 MET cc_start: 0.4999 (mtt) cc_final: 0.4650 (mpp) REVERT: E 37 GLU cc_start: 0.7874 (pp20) cc_final: 0.7561 (pp20) REVERT: E 112 MET cc_start: 0.8899 (mtp) cc_final: 0.8684 (mtm) REVERT: E 125 GLU cc_start: 0.8241 (tt0) cc_final: 0.7958 (tt0) REVERT: E 264 THR cc_start: 0.8938 (m) cc_final: 0.8707 (p) REVERT: H 38 HIS cc_start: 0.8414 (m170) cc_final: 0.8093 (m90) REVERT: H 93 ASP cc_start: 0.8497 (m-30) cc_final: 0.7978 (m-30) REVERT: L 80 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7877 (mm-40) REVERT: F 70 ARG cc_start: 0.7906 (mtm110) cc_final: 0.6951 (ptt180) outliers start: 51 outliers final: 30 residues processed: 424 average time/residue: 0.2761 time to fit residues: 179.6865 Evaluate side-chains 427 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 392 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 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 L residue 34 VAL 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: 0.8980 chunk 172 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 chunk 137 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** E 134 ASN H 80 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.173628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.147427 restraints weight = 24242.786| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.24 r_work: 0.3423 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1459 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= 0.138 Angle : 0.560 8.507 25059 Z= 0.289 Chirality : 0.042 0.164 2823 Planarity : 0.004 0.052 3137 Dihedral : 4.321 25.442 2446 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 2.23 % Allowed : 16.05 % Favored : 81.72 % 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: 1.02 (0.19), residues: 2180 helix: 2.27 (0.17), residues: 958 sheet: 0.81 (0.25), residues: 433 loop : -1.51 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 50 HIS 0.005 0.001 HIS B 212 PHE 0.021 0.001 PHE C 306 TYR 0.018 0.001 TYR L 50 ARG 0.006 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1074) hydrogen bonds : angle 4.49568 ( 3090) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.77047 ( 8) covalent geometry : bond 0.00318 (18471) covalent geometry : angle 0.56004 (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 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 402 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8212 (pt0) cc_final: 0.7706 (pt0) REVERT: A 189 ASP cc_start: 0.7278 (t0) cc_final: 0.6981 (t0) REVERT: A 205 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7421 (mtpp) REVERT: A 230 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6439 (mm-30) REVERT: A 276 LEU cc_start: 0.7613 (mt) cc_final: 0.7309 (mt) REVERT: B 79 PHE cc_start: 0.7288 (t80) cc_final: 0.6854 (t80) REVERT: B 133 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7448 (tptp) REVERT: B 186 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6884 (mm-30) REVERT: B 192 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8580 (mp) REVERT: B 193 ASP cc_start: 0.7864 (t0) cc_final: 0.7513 (t0) REVERT: B 230 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 260 GLN cc_start: 0.7165 (tt0) cc_final: 0.6920 (tt0) REVERT: B 296 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 306 PHE cc_start: 0.7416 (t80) cc_final: 0.7038 (t80) REVERT: C 193 ASP cc_start: 0.8064 (t0) cc_final: 0.7792 (t0) REVERT: C 289 GLU cc_start: 0.7709 (tt0) cc_final: 0.7399 (tt0) REVERT: D 197 GLU cc_start: 0.7797 (tp30) cc_final: 0.6560 (tm-30) REVERT: D 226 TRP cc_start: 0.8304 (m100) cc_final: 0.7843 (m100) REVERT: D 232 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8361 (mm) REVERT: E 37 GLU cc_start: 0.7877 (pp20) cc_final: 0.7572 (pp20) REVERT: E 232 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8420 (mm) REVERT: H 9 GLU cc_start: 0.6329 (mp0) cc_final: 0.5799 (mp0) REVERT: H 38 HIS cc_start: 0.8355 (m170) cc_final: 0.7909 (m90) REVERT: H 93 ASP cc_start: 0.8456 (m-30) cc_final: 0.7980 (m-30) REVERT: H 120 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: L 80 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7893 (mm-40) REVERT: F 70 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7030 (ptt180) outliers start: 45 outliers final: 32 residues processed: 424 average time/residue: 0.2563 time to fit residues: 169.5739 Evaluate side-chains 426 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 145 ASP 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 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 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: 0.5980 chunk 65 optimal weight: 0.0980 chunk 110 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.173162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146727 restraints weight = 24285.694| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.26 r_work: 0.3417 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18475 Z= 0.148 Angle : 0.565 8.791 25059 Z= 0.291 Chirality : 0.043 0.294 2823 Planarity : 0.004 0.052 3137 Dihedral : 4.332 24.971 2446 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 2.87 % Allowed : 17.09 % Favored : 80.04 % 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: 1.02 (0.18), residues: 2180 helix: 2.28 (0.17), residues: 958 sheet: 0.80 (0.25), residues: 433 loop : -1.52 (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 0.013 0.001 PHE E 79 TYR 0.017 0.001 TYR L 50 ARG 0.004 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1074) hydrogen bonds : angle 4.48868 ( 3090) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.73865 ( 8) covalent geometry : bond 0.00343 (18471) covalent geometry : angle 0.56468 (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: 58 poor density : 391 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8269 (pt0) cc_final: 0.7729 (pt0) REVERT: A 189 ASP cc_start: 0.7261 (t0) cc_final: 0.6964 (t0) REVERT: A 205 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7483 (mtpp) REVERT: A 230 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6406 (mm-30) REVERT: A 232 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 276 LEU cc_start: 0.7618 (mt) cc_final: 0.7295 (mt) REVERT: B 79 PHE cc_start: 0.7305 (t80) cc_final: 0.6883 (t80) REVERT: B 133 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7443 (tptp) REVERT: B 186 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 192 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8590 (mp) REVERT: B 193 ASP cc_start: 0.7873 (t0) cc_final: 0.7522 (t0) REVERT: B 230 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 260 GLN cc_start: 0.7163 (tt0) cc_final: 0.6951 (tt0) REVERT: B 296 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 306 PHE cc_start: 0.7388 (t80) cc_final: 0.7048 (t80) REVERT: C 193 ASP cc_start: 0.8064 (t0) cc_final: 0.7780 (t0) REVERT: C 289 GLU cc_start: 0.7709 (tt0) cc_final: 0.7410 (tt0) REVERT: D 232 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8369 (mm) REVERT: E 37 GLU cc_start: 0.7892 (pp20) cc_final: 0.7569 (pp20) REVERT: E 70 THR cc_start: 0.8075 (p) cc_final: 0.7798 (m) REVERT: E 232 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8425 (mm) REVERT: H 9 GLU cc_start: 0.6357 (mp0) cc_final: 0.5776 (mp0) REVERT: H 38 HIS cc_start: 0.8340 (m170) cc_final: 0.7896 (m90) REVERT: H 93 ASP cc_start: 0.8445 (m-30) cc_final: 0.7964 (m-30) REVERT: H 120 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: L 80 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7944 (mm-40) REVERT: F 70 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7052 (ptt180) outliers start: 58 outliers final: 41 residues processed: 423 average time/residue: 0.2635 time to fit residues: 174.2887 Evaluate side-chains 432 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 384 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain 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 132 THR 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 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 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 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 154 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** E 134 ASN H 80 ASN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.172626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146337 restraints weight = 24123.719| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.24 r_work: 0.3414 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1643 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= 0.149 Angle : 0.568 10.749 25059 Z= 0.292 Chirality : 0.043 0.195 2823 Planarity : 0.004 0.052 3137 Dihedral : 4.337 24.580 2446 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 2.77 % Allowed : 17.73 % 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 (0.17), residues: 958 sheet: 0.76 (0.25), residues: 433 loop : -1.52 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.012 0.001 PHE E 79 TYR 0.016 0.001 TYR L 56 ARG 0.007 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 1074) hydrogen bonds : angle 4.46265 ( 3090) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.78863 ( 8) covalent geometry : bond 0.00346 (18471) covalent geometry : angle 0.56768 (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 454 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 398 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7362 (t70) cc_final: 0.6878 (m-30) REVERT: A 27 PHE cc_start: 0.8177 (t80) cc_final: 0.7846 (t80) REVERT: A 30 GLU cc_start: 0.8287 (pt0) cc_final: 0.7725 (pt0) REVERT: A 189 ASP cc_start: 0.7243 (t0) cc_final: 0.6964 (t0) REVERT: A 205 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7496 (mtpp) REVERT: A 230 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6457 (mm-30) REVERT: A 232 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 276 LEU cc_start: 0.7631 (mt) cc_final: 0.7345 (mt) REVERT: B 79 PHE cc_start: 0.7282 (t80) cc_final: 0.6889 (t80) REVERT: B 133 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7402 (tptp) REVERT: B 156 TYR cc_start: 0.6257 (m-10) cc_final: 0.6006 (m-10) REVERT: B 165 ARG cc_start: 0.7137 (mmm-85) cc_final: 0.6931 (mmm-85) REVERT: B 186 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6949 (mm-30) REVERT: B 192 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 193 ASP cc_start: 0.7868 (t0) cc_final: 0.7528 (t0) REVERT: B 230 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 260 GLN cc_start: 0.7182 (tt0) cc_final: 0.6969 (tt0) REVERT: B 296 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 193 ASP cc_start: 0.8069 (t0) cc_final: 0.7783 (t0) REVERT: D 226 TRP cc_start: 0.8311 (m100) cc_final: 0.7859 (m100) REVERT: D 232 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8340 (mm) REVERT: E 70 THR cc_start: 0.8086 (p) cc_final: 0.7797 (m) REVERT: E 232 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8376 (mm) REVERT: H 9 GLU cc_start: 0.6544 (mp0) cc_final: 0.5927 (mp0) REVERT: H 38 HIS cc_start: 0.8359 (m170) cc_final: 0.7921 (m90) REVERT: H 93 ASP cc_start: 0.8448 (m-30) cc_final: 0.7971 (m-30) REVERT: H 120 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7970 (mtm) REVERT: L 80 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7957 (mm-40) REVERT: F 70 ARG cc_start: 0.7924 (mtm110) cc_final: 0.6987 (ptt180) outliers start: 56 outliers final: 42 residues processed: 429 average time/residue: 0.2650 time to fit residues: 176.9744 Evaluate side-chains 436 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 387 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 130 ILE 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 28 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 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 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 134 ASN 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 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 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 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: 0.4980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 L 39 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.169305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.142768 restraints weight = 24132.040| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.23 r_work: 0.3368 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18475 Z= 0.229 Angle : 0.625 10.580 25059 Z= 0.321 Chirality : 0.045 0.191 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.500 24.636 2446 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.37 % Allowed : 18.28 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.18), residues: 2180 helix: 2.12 (0.16), residues: 958 sheet: 0.54 (0.25), residues: 445 loop : -1.54 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 PHE 0.019 0.002 PHE H 71 TYR 0.022 0.002 TYR C 236 ARG 0.007 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1074) hydrogen bonds : angle 4.62577 ( 3090) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.99498 ( 8) covalent geometry : bond 0.00545 (18471) covalent geometry : angle 0.62476 (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 461 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 2.151 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7324 (t70) cc_final: 0.6926 (m-30) REVERT: A 27 PHE cc_start: 0.8237 (t80) cc_final: 0.7889 (t80) REVERT: A 30 GLU cc_start: 0.8304 (pt0) cc_final: 0.7740 (pt0) REVERT: A 189 ASP cc_start: 0.7281 (t0) cc_final: 0.6976 (t0) REVERT: A 230 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 232 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 276 LEU cc_start: 0.7692 (mt) cc_final: 0.7422 (mt) REVERT: B 38 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6372 (mm-30) REVERT: B 133 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7387 (tptp) REVERT: B 156 TYR cc_start: 0.6297 (m-10) cc_final: 0.6070 (m-10) REVERT: B 186 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 192 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 193 ASP cc_start: 0.7964 (t0) cc_final: 0.7584 (t0) REVERT: B 260 GLN cc_start: 0.7238 (tt0) cc_final: 0.7036 (tt0) REVERT: B 296 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 306 PHE cc_start: 0.7434 (t80) cc_final: 0.7041 (t80) REVERT: C 193 ASP cc_start: 0.8123 (t0) cc_final: 0.7835 (t0) REVERT: C 289 GLU cc_start: 0.7782 (tt0) cc_final: 0.7380 (tt0) REVERT: D 232 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8396 (mm) REVERT: D 237 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7715 (mmt90) REVERT: E 162 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8143 (tpt90) REVERT: E 232 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8468 (mm) REVERT: H 38 HIS cc_start: 0.8476 (m170) cc_final: 0.8030 (m90) REVERT: H 93 ASP cc_start: 0.8436 (m-30) cc_final: 0.7986 (m-30) REVERT: H 120 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8006 (mtm) REVERT: L 80 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7956 (mm-40) REVERT: F 50 TRP cc_start: 0.8550 (t60) cc_final: 0.8195 (t60) REVERT: F 70 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7029 (ptt180) outliers start: 68 outliers final: 48 residues processed: 431 average time/residue: 0.2686 time to fit residues: 178.2795 Evaluate side-chains 451 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 395 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 130 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 287 THR 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 265 VAL Chi-restraints excluded: chain D residue 287 THR 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 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 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 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: 5.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 GLN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 285 ASN E 314 ASN H 80 ASN L 39 GLN G 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144283 restraints weight = 24227.638| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.25 r_work: 0.3399 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18475 Z= 0.162 Angle : 0.602 11.544 25059 Z= 0.309 Chirality : 0.043 0.202 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.468 24.467 2446 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.87 % Allowed : 19.07 % Favored : 78.06 % 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: 2.22 (0.16), residues: 956 sheet: 0.62 (0.25), residues: 437 loop : -1.57 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 39 HIS 0.009 0.001 HIS C 83 PHE 0.024 0.001 PHE C 306 TYR 0.026 0.001 TYR B 255 ARG 0.007 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1074) hydrogen bonds : angle 4.57543 ( 3090) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.74894 ( 8) covalent geometry : bond 0.00382 (18471) covalent geometry : angle 0.60203 (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 442 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 384 time to evaluate : 1.966 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7273 (t70) cc_final: 0.6938 (m-30) REVERT: A 27 PHE cc_start: 0.8197 (t80) cc_final: 0.7870 (t80) REVERT: A 30 GLU cc_start: 0.8280 (pt0) cc_final: 0.7676 (pt0) REVERT: A 189 ASP cc_start: 0.7261 (t0) cc_final: 0.6976 (t0) REVERT: A 205 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7446 (mtpp) REVERT: A 230 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6462 (mm-30) REVERT: A 232 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 276 LEU cc_start: 0.7652 (mt) cc_final: 0.7367 (mt) REVERT: B 38 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6416 (mm-30) REVERT: B 79 PHE cc_start: 0.7312 (t80) cc_final: 0.6881 (t80) REVERT: B 133 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7390 (tptp) REVERT: B 186 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 192 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 193 ASP cc_start: 0.7969 (t0) cc_final: 0.7580 (t0) REVERT: B 292 LYS cc_start: 0.7558 (mttp) cc_final: 0.7230 (tttp) REVERT: B 296 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 306 PHE cc_start: 0.7458 (t80) cc_final: 0.7033 (t80) REVERT: C 193 ASP cc_start: 0.8101 (t0) cc_final: 0.7811 (t0) REVERT: C 301 PHE cc_start: 0.8268 (m-10) cc_final: 0.8031 (m-10) REVERT: D 226 TRP cc_start: 0.8274 (m100) cc_final: 0.7862 (m100) REVERT: D 232 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8386 (mm) REVERT: D 237 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7718 (mmt90) REVERT: E 232 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8450 (mm) REVERT: E 314 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.5272 (m110) REVERT: H 38 HIS cc_start: 0.8439 (m170) cc_final: 0.7998 (m90) REVERT: H 93 ASP cc_start: 0.8427 (m-30) cc_final: 0.7992 (m-30) REVERT: H 120 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8025 (mtm) REVERT: F 70 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7127 (ptt180) outliers start: 58 outliers final: 45 residues processed: 416 average time/residue: 0.2707 time to fit residues: 174.2268 Evaluate side-chains 426 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 130 ILE 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 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain 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 265 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 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 110 THR Chi-restraints excluded: chain H residue 120 MET 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 F residue 125 GLN 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: 0.9980 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 314 ASN H 80 ASN L 39 GLN L 80 GLN G 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.170146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.143715 restraints weight = 24206.483| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.23 r_work: 0.3385 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18475 Z= 0.181 Angle : 0.627 13.099 25059 Z= 0.319 Chirality : 0.044 0.210 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.480 24.401 2446 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 2.87 % Allowed : 19.17 % Favored : 77.96 % 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: 2.18 (0.16), residues: 956 sheet: 0.58 (0.25), residues: 439 loop : -1.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 39 HIS 0.008 0.001 HIS C 83 PHE 0.025 0.002 PHE C 306 TYR 0.027 0.002 TYR B 255 ARG 0.007 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1074) hydrogen bonds : angle 4.60907 ( 3090) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.77579 ( 8) covalent geometry : bond 0.00429 (18471) covalent geometry : angle 0.62685 (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 438 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 380 time to evaluate : 1.986 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8273 (pt0) cc_final: 0.7723 (pt0) REVERT: A 189 ASP cc_start: 0.7294 (t0) cc_final: 0.6998 (t0) REVERT: A 230 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6491 (mm-30) REVERT: A 232 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 276 LEU cc_start: 0.7644 (mt) cc_final: 0.7355 (mt) REVERT: B 38 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 79 PHE cc_start: 0.7309 (t80) cc_final: 0.6883 (t80) REVERT: B 133 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7377 (tptp) REVERT: B 186 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 192 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 193 ASP cc_start: 0.7977 (t0) cc_final: 0.7593 (t0) REVERT: B 242 LEU cc_start: 0.7514 (mt) cc_final: 0.7311 (tp) REVERT: B 292 LYS cc_start: 0.7470 (mttp) cc_final: 0.7152 (tttp) REVERT: B 296 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 306 PHE cc_start: 0.7482 (t80) cc_final: 0.7049 (t80) REVERT: C 193 ASP cc_start: 0.8109 (t0) cc_final: 0.7818 (t0) REVERT: C 301 PHE cc_start: 0.8197 (m-10) cc_final: 0.7948 (m-80) REVERT: C 334 MET cc_start: 0.7654 (ttp) cc_final: 0.7449 (ttp) REVERT: D 226 TRP cc_start: 0.8289 (m100) cc_final: 0.7884 (m100) REVERT: D 232 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8390 (mm) REVERT: D 237 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7742 (mmt90) REVERT: E 232 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8453 (mm) REVERT: E 314 ASN cc_start: 0.5639 (OUTLIER) cc_final: 0.5245 (m110) REVERT: H 38 HIS cc_start: 0.8476 (m170) cc_final: 0.8031 (m90) REVERT: H 93 ASP cc_start: 0.8428 (m-30) cc_final: 0.7989 (m-30) REVERT: H 120 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8072 (mtm) REVERT: F 50 TRP cc_start: 0.8551 (t60) cc_final: 0.8182 (t60) REVERT: F 70 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7004 (ptt180) outliers start: 58 outliers final: 47 residues processed: 411 average time/residue: 0.2752 time to fit residues: 175.2290 Evaluate side-chains 429 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 130 ILE 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 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 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 265 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 ASN 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 110 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 12 LEU 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 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: 0.9990 chunk 52 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 39 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.171750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.145779 restraints weight = 24168.730| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.21 r_work: 0.3395 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 18475 Z= 0.225 Angle : 0.882 59.200 25059 Z= 0.507 Chirality : 0.047 0.899 2823 Planarity : 0.006 0.140 3137 Dihedral : 4.487 24.380 2446 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 2.77 % Allowed : 18.87 % Favored : 78.36 % Cbeta Deviations : 0.10 % 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: 2.18 (0.16), residues: 956 sheet: 0.57 (0.25), residues: 439 loop : -1.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 39 HIS 0.006 0.001 HIS C 83 PHE 0.022 0.001 PHE C 306 TYR 0.024 0.001 TYR B 255 ARG 0.006 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 1074) hydrogen bonds : angle 4.60874 ( 3090) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.28774 ( 8) covalent geometry : bond 0.00493 (18471) covalent geometry : angle 0.88179 (25051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8778.78 seconds wall clock time: 153 minutes 0.76 seconds (9180.76 seconds total)