Starting phenix.real_space_refine on Wed Jul 30 02:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2025/8r3g_18864.cif" } resolution = 4.4 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Se 48 7.20 5 P 82 5.49 5 S 8 5.16 5 C 7285 2.51 5 N 2090 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11985 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Restraints were copied for chains: D, C Time building chain proxies: 10.22, per 1000 atoms: 0.85 Number of scatterers: 11985 At special positions: 0 Unit cell: (146.316, 130.698, 88.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 48 33.99 S 8 16.00 P 82 15.00 O 2472 8.00 N 2090 7.00 C 7285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 61.3% alpha, 13.1% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 12 through 33 Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 74 through 92 removed outlier: 5.160A pdb=" N ASP C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP C 296 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.683A pdb=" N LYS A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 47 through 61 Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 33 Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 74 through 92 removed outlier: 5.159A pdb=" N ASP B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.705A pdb=" N VAL B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.705A pdb=" N ASP B 296 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.682A pdb=" N LYS D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 4.161A pdb=" N LYS D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 185 through 198 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP D 296 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 318 Processing helix chain 'D' and resid 330 through 338 Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 67 Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP C 109 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 328 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 111 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 301 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 329 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 237 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 304 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS C 239 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 242 through 243 removed outlier: 6.768A pdb=" N PHE C 275 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 269 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN C 276 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 281 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP A 109 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 328 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 111 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 301 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP A 329 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 237 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 304 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 239 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE A 275 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 269 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 276 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 281 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP B 109 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 328 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 111 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 301 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASP B 329 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 237 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 304 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS B 239 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE B 275 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 269 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN B 276 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 281 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 67 Processing sheet with id=AB2, first strand: chain 'D' and resid 109 through 113 removed outlier: 6.556A pdb=" N ASP D 109 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 328 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 111 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 301 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP D 329 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 237 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL D 304 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS D 239 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE D 275 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU D 269 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN D 276 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 281 " --> pdb=" O ASN D 276 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3703 1.35 - 1.51: 3821 1.51 - 1.67: 4676 1.67 - 1.84: 8 1.84 - 2.00: 96 Bond restraints: 12304 Sorted by residual: bond pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.13e+01 bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.10e+01 bond pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N LEU B 107 " pdb=" CA LEU B 107 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.25e-02 6.40e+03 1.75e+01 ... (remaining 12299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14551 2.15 - 4.30: 2117 4.30 - 6.45: 205 6.45 - 8.60: 22 8.60 - 10.74: 28 Bond angle restraints: 16923 Sorted by residual: angle pdb=" C PHE C 205 " pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE B 205 " pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE D 205 " pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 122.59 116.43 6.16 7.20e-01 1.93e+00 7.31e+01 angle pdb=" C PHE A 205 " pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 122.59 116.46 6.13 7.20e-01 1.93e+00 7.24e+01 angle pdb=" N ARG B 175 " pdb=" CA ARG B 175 " pdb=" C ARG B 175 " ideal model delta sigma weight residual 110.53 99.79 10.74 1.32e+00 5.74e-01 6.62e+01 ... (remaining 16918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6931 35.97 - 71.93: 435 71.93 - 107.90: 18 107.90 - 143.87: 0 143.87 - 179.84: 2 Dihedral angle restraints: 7386 sinusoidal: 3546 harmonic: 3840 Sorted by residual: dihedral pdb=" C4' DC E 19 " pdb=" C3' DC E 19 " pdb=" O3' DC E 19 " pdb=" P DA E 20 " ideal model delta sinusoidal sigma weight residual 220.00 40.16 179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC F 19 " pdb=" C3' DC F 19 " pdb=" O3' DC F 19 " pdb=" P DC F 20 " ideal model delta sinusoidal sigma weight residual 220.00 43.75 176.25 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C MSE D 88 " pdb=" N MSE D 88 " pdb=" CA MSE D 88 " pdb=" CB MSE D 88 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 7383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1275 0.084 - 0.169: 549 0.169 - 0.253: 107 0.253 - 0.337: 38 0.337 - 0.422: 11 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA VAL D 325 " pdb=" N VAL D 325 " pdb=" C VAL D 325 " pdb=" CB VAL D 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA VAL A 325 " pdb=" N VAL A 325 " pdb=" C VAL A 325 " pdb=" CB VAL A 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA VAL C 325 " pdb=" N VAL C 325 " pdb=" C VAL C 325 " pdb=" CB VAL C 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1977 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR D 87 " -0.083 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.032 2.00e-02 2.50e+03 pdb=" N MSE D 88 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 87 " -0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR A 87 " 0.083 2.00e-02 2.50e+03 pdb=" O THR A 87 " -0.032 2.00e-02 2.50e+03 pdb=" N MSE A 88 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 174 " 0.019 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA A 174 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A 174 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 175 " 0.024 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1547 2.77 - 3.31: 11645 3.31 - 3.84: 20868 3.84 - 4.37: 26612 4.37 - 4.90: 39448 Nonbonded interactions: 100120 Sorted by model distance: nonbonded pdb=" OE2 GLU B 33 " pdb=" OH TYR B 78 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU C 33 " pdb=" OH TYR C 78 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG C 49 " pdb=" N6 DA E 28 " model vdw 2.253 3.200 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 78 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU D 33 " pdb=" OH TYR D 78 " model vdw 2.259 3.040 ... (remaining 100115 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 39.600 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5193 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 : 0.013 0.099 12304 Z= 0.853 Angle : 1.540 10.744 16923 Z= 1.067 Chirality : 0.100 0.422 1980 Planarity : 0.007 0.048 1878 Dihedral : 19.042 179.837 4906 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.19 (0.21), residues: 1324 helix: -0.91 (0.16), residues: 732 sheet: -0.59 (0.35), residues: 156 loop : -0.21 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP C 122 HIS 0.015 0.005 HIS C 239 PHE 0.028 0.006 PHE B 57 TYR 0.049 0.010 TYR A 317 ARG 0.011 0.002 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.18693 ( 694) hydrogen bonds : angle 7.14085 ( 1893) covalent geometry : bond 0.01344 (12304) covalent geometry : angle 1.54038 (16923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 GLN cc_start: 0.8013 (mt0) cc_final: 0.7503 (mm-40) REVERT: C 132 VAL cc_start: 0.8206 (t) cc_final: 0.7907 (p) REVERT: C 152 THR cc_start: 0.8581 (m) cc_final: 0.8272 (p) REVERT: C 173 PRO cc_start: 0.6274 (Cg_endo) cc_final: 0.5881 (Cg_exo) REVERT: C 304 VAL cc_start: 0.7403 (t) cc_final: 0.7123 (m) REVERT: A 145 VAL cc_start: 0.7381 (t) cc_final: 0.6907 (t) REVERT: B 29 ILE cc_start: 0.8635 (mt) cc_final: 0.8279 (mm) REVERT: B 35 ILE cc_start: 0.8725 (tt) cc_final: 0.8216 (tp) REVERT: B 101 LEU cc_start: 0.7635 (tp) cc_final: 0.7323 (tp) REVERT: B 132 VAL cc_start: 0.8259 (t) cc_final: 0.7993 (p) REVERT: B 152 THR cc_start: 0.8727 (m) cc_final: 0.8385 (p) REVERT: B 304 VAL cc_start: 0.7346 (t) cc_final: 0.7090 (m) REVERT: D 12 LEU cc_start: 0.8142 (mt) cc_final: 0.6583 (mt) REVERT: D 19 MSE cc_start: 0.5088 (mtp) cc_final: 0.4762 (ttp) REVERT: D 145 VAL cc_start: 0.7443 (t) cc_final: 0.7094 (t) REVERT: D 295 ILE cc_start: 0.8004 (pt) cc_final: 0.7693 (pt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.2818 time to fit residues: 150.4163 Evaluate side-chains 203 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN A 252 ASN B 3 GLN B 6 GLN D 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.087358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.069900 restraints weight = 50810.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072480 restraints weight = 32358.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074540 restraints weight = 22672.633| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12304 Z= 0.208 Angle : 0.710 9.206 16923 Z= 0.387 Chirality : 0.044 0.186 1980 Planarity : 0.005 0.100 1878 Dihedral : 20.694 178.469 2326 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.53 (0.22), residues: 1324 helix: 0.84 (0.18), residues: 764 sheet: -0.27 (0.35), residues: 154 loop : -0.09 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 122 HIS 0.006 0.002 HIS B 192 PHE 0.032 0.003 PHE D 139 TYR 0.017 0.002 TYR C 274 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 694) hydrogen bonds : angle 4.78530 ( 1893) covalent geometry : bond 0.00443 (12304) covalent geometry : angle 0.70994 (16923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8868 (mp) cc_final: 0.8116 (mp) REVERT: C 35 ILE cc_start: 0.7801 (mm) cc_final: 0.7428 (mm) REVERT: C 54 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8334 (mm-30) REVERT: C 92 LEU cc_start: 0.7077 (mt) cc_final: 0.6823 (mt) REVERT: C 125 LYS cc_start: 0.8257 (mttm) cc_final: 0.8032 (tttt) REVERT: C 201 TYR cc_start: 0.6470 (p90) cc_final: 0.6001 (p90) REVERT: C 304 VAL cc_start: 0.8970 (t) cc_final: 0.8504 (m) REVERT: A 12 LEU cc_start: 0.9402 (mp) cc_final: 0.9093 (mp) REVERT: A 175 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8454 (tpp80) REVERT: A 236 MSE cc_start: 0.4967 (mtm) cc_final: 0.2918 (mtm) REVERT: B 54 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 132 VAL cc_start: 0.9588 (t) cc_final: 0.9160 (p) REVERT: B 201 TYR cc_start: 0.6299 (p90) cc_final: 0.5945 (p90) REVERT: B 304 VAL cc_start: 0.8922 (t) cc_final: 0.8340 (m) REVERT: B 327 VAL cc_start: 0.9007 (t) cc_final: 0.8733 (t) REVERT: D 12 LEU cc_start: 0.9027 (mt) cc_final: 0.8735 (mp) REVERT: D 175 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8576 (tpp80) REVERT: D 236 MSE cc_start: 0.4905 (mtm) cc_final: 0.2954 (mtm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2588 time to fit residues: 90.4306 Evaluate side-chains 160 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 0.0970 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.087164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.069647 restraints weight = 53536.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.072324 restraints weight = 33250.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.074467 restraints weight = 23005.146| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12304 Z= 0.138 Angle : 0.588 8.029 16923 Z= 0.322 Chirality : 0.041 0.197 1980 Planarity : 0.004 0.067 1878 Dihedral : 20.550 179.527 2326 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.23), residues: 1324 helix: 1.38 (0.18), residues: 758 sheet: 0.11 (0.36), residues: 158 loop : -0.28 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 122 HIS 0.002 0.001 HIS B 283 PHE 0.021 0.002 PHE D 271 TYR 0.011 0.001 TYR A 215 ARG 0.003 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 694) hydrogen bonds : angle 4.35682 ( 1893) covalent geometry : bond 0.00293 (12304) covalent geometry : angle 0.58844 (16923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 132 VAL cc_start: 0.9518 (t) cc_final: 0.9308 (p) REVERT: C 247 MSE cc_start: 0.4440 (mmm) cc_final: 0.3184 (mmp) REVERT: A 12 LEU cc_start: 0.9354 (mp) cc_final: 0.9112 (mt) REVERT: A 51 LEU cc_start: 0.9124 (tp) cc_final: 0.8582 (mt) REVERT: A 175 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8172 (tpp80) REVERT: A 327 VAL cc_start: 0.8602 (p) cc_final: 0.8315 (m) REVERT: B 15 LEU cc_start: 0.9110 (mp) cc_final: 0.8065 (mm) REVERT: B 54 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 88 MSE cc_start: 0.8374 (tpp) cc_final: 0.7675 (tpp) REVERT: B 92 LEU cc_start: 0.7000 (mt) cc_final: 0.6654 (mt) REVERT: B 132 VAL cc_start: 0.9592 (t) cc_final: 0.9323 (p) REVERT: B 148 THR cc_start: 0.8630 (t) cc_final: 0.8391 (t) REVERT: B 241 ILE cc_start: 0.8355 (mm) cc_final: 0.8112 (mm) REVERT: D 12 LEU cc_start: 0.8987 (mt) cc_final: 0.8747 (mp) REVERT: D 51 LEU cc_start: 0.9069 (tp) cc_final: 0.8530 (mt) REVERT: D 175 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8291 (tpp80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2380 time to fit residues: 73.6683 Evaluate side-chains 158 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.079630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062841 restraints weight = 58111.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.065402 restraints weight = 35831.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.067320 restraints weight = 24606.389| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12304 Z= 0.204 Angle : 0.630 6.760 16923 Z= 0.352 Chirality : 0.042 0.148 1980 Planarity : 0.005 0.068 1878 Dihedral : 20.579 176.769 2326 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.72 (0.23), residues: 1324 helix: 1.12 (0.18), residues: 764 sheet: 0.20 (0.37), residues: 152 loop : -0.49 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 122 HIS 0.005 0.001 HIS B 192 PHE 0.031 0.003 PHE A 139 TYR 0.022 0.002 TYR B 201 ARG 0.006 0.001 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 694) hydrogen bonds : angle 4.79103 ( 1893) covalent geometry : bond 0.00427 (12304) covalent geometry : angle 0.62952 (16923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ILE cc_start: 0.7860 (mm) cc_final: 0.7634 (mm) REVERT: C 92 LEU cc_start: 0.7252 (mt) cc_final: 0.6955 (mt) REVERT: C 148 THR cc_start: 0.8831 (t) cc_final: 0.8582 (t) REVERT: C 160 MSE cc_start: 0.4475 (tpp) cc_final: 0.4153 (tpp) REVERT: C 268 THR cc_start: 0.8343 (t) cc_final: 0.8024 (m) REVERT: A 51 LEU cc_start: 0.9020 (tp) cc_final: 0.8784 (mt) REVERT: A 139 PHE cc_start: 0.7291 (m-80) cc_final: 0.7023 (m-80) REVERT: A 175 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8009 (tpp80) REVERT: A 327 VAL cc_start: 0.8673 (p) cc_final: 0.7857 (m) REVERT: B 88 MSE cc_start: 0.8427 (tpp) cc_final: 0.8161 (tpp) REVERT: B 160 MSE cc_start: 0.4402 (tpp) cc_final: 0.3681 (mmm) REVERT: B 237 LEU cc_start: 0.9153 (tp) cc_final: 0.8920 (tp) REVERT: D 12 LEU cc_start: 0.9117 (mt) cc_final: 0.8752 (mp) REVERT: D 51 LEU cc_start: 0.9032 (tp) cc_final: 0.8795 (mt) REVERT: D 175 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.7931 (tpp80) REVERT: D 327 VAL cc_start: 0.8597 (p) cc_final: 0.7894 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2164 time to fit residues: 57.3467 Evaluate side-chains 135 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.082414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065742 restraints weight = 52864.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068377 restraints weight = 32382.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.070356 restraints weight = 22021.427| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12304 Z= 0.126 Angle : 0.551 8.335 16923 Z= 0.305 Chirality : 0.039 0.133 1980 Planarity : 0.004 0.064 1878 Dihedral : 20.466 179.288 2326 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.96 (0.23), residues: 1324 helix: 1.46 (0.19), residues: 756 sheet: 0.21 (0.37), residues: 154 loop : -0.65 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 122 HIS 0.002 0.000 HIS C 283 PHE 0.028 0.003 PHE A 139 TYR 0.010 0.001 TYR C 28 ARG 0.003 0.000 ARG D 250 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 694) hydrogen bonds : angle 4.41477 ( 1893) covalent geometry : bond 0.00269 (12304) covalent geometry : angle 0.55057 (16923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 TRP cc_start: 0.7712 (p90) cc_final: 0.7402 (p90) REVERT: C 154 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7881 (tp30) REVERT: C 268 THR cc_start: 0.7897 (t) cc_final: 0.7588 (m) REVERT: A 19 MSE cc_start: 0.5820 (ptm) cc_final: 0.4534 (ptp) REVERT: A 135 MSE cc_start: 0.5063 (tpp) cc_final: 0.4652 (tpp) REVERT: A 154 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8724 (mt-10) REVERT: A 175 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.7988 (tpp80) REVERT: A 327 VAL cc_start: 0.7910 (p) cc_final: 0.7164 (p) REVERT: B 88 MSE cc_start: 0.8396 (tpp) cc_final: 0.8150 (tpp) REVERT: B 120 SER cc_start: 0.8506 (p) cc_final: 0.8062 (m) REVERT: B 239 HIS cc_start: 0.7716 (p-80) cc_final: 0.7485 (p-80) REVERT: D 12 LEU cc_start: 0.8991 (mt) cc_final: 0.8574 (mp) REVERT: D 135 MSE cc_start: 0.7695 (tpp) cc_final: 0.6847 (tpp) REVERT: D 175 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7717 (tpp80) REVERT: D 236 MSE cc_start: 0.4002 (mtp) cc_final: 0.2520 (mtp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2256 time to fit residues: 63.9714 Evaluate side-chains 144 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 6 GLN D 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.076611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.060537 restraints weight = 56680.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063002 restraints weight = 34719.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064882 restraints weight = 23666.681| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12304 Z= 0.240 Angle : 0.682 7.671 16923 Z= 0.378 Chirality : 0.042 0.151 1980 Planarity : 0.005 0.070 1878 Dihedral : 20.632 176.641 2326 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.15 (0.22), residues: 1324 helix: 0.69 (0.18), residues: 778 sheet: -0.15 (0.37), residues: 148 loop : -0.78 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 122 HIS 0.005 0.001 HIS B 192 PHE 0.042 0.004 PHE A 139 TYR 0.018 0.002 TYR B 28 ARG 0.006 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 694) hydrogen bonds : angle 5.12194 ( 1893) covalent geometry : bond 0.00510 (12304) covalent geometry : angle 0.68216 (16923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 LEU cc_start: 0.9167 (tp) cc_final: 0.8798 (tp) REVERT: C 122 TRP cc_start: 0.8006 (p90) cc_final: 0.7050 (p90) REVERT: C 193 MSE cc_start: 0.7345 (ttp) cc_final: 0.7061 (ttp) REVERT: C 237 LEU cc_start: 0.9230 (tp) cc_final: 0.8841 (tp) REVERT: A 175 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8109 (tpp80) REVERT: A 327 VAL cc_start: 0.7829 (p) cc_final: 0.7195 (m) REVERT: B 122 TRP cc_start: 0.7948 (p90) cc_final: 0.7646 (p90) REVERT: D 12 LEU cc_start: 0.9165 (mt) cc_final: 0.8869 (mp) REVERT: D 175 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.8013 (tpp80) REVERT: D 274 TYR cc_start: 0.7558 (m-80) cc_final: 0.7241 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2037 time to fit residues: 52.0745 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 0.0040 chunk 136 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.082253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.066435 restraints weight = 54829.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068871 restraints weight = 34533.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.070744 restraints weight = 24093.099| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12304 Z= 0.134 Angle : 0.580 9.797 16923 Z= 0.318 Chirality : 0.039 0.138 1980 Planarity : 0.004 0.066 1878 Dihedral : 20.501 179.742 2326 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.57 (0.23), residues: 1324 helix: 1.20 (0.18), residues: 772 sheet: -0.37 (0.37), residues: 156 loop : -0.82 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.003 0.001 HIS D 286 PHE 0.023 0.002 PHE D 271 TYR 0.009 0.001 TYR A 317 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 694) hydrogen bonds : angle 4.56565 ( 1893) covalent geometry : bond 0.00294 (12304) covalent geometry : angle 0.57969 (16923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 TRP cc_start: 0.7352 (p90) cc_final: 0.7038 (p90) REVERT: C 237 LEU cc_start: 0.9051 (tp) cc_final: 0.8780 (tp) REVERT: A 108 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7357 (tptt) REVERT: A 175 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.7997 (tpp80) REVERT: A 274 TYR cc_start: 0.7502 (m-80) cc_final: 0.7249 (m-80) REVERT: B 62 ASN cc_start: 0.9149 (m110) cc_final: 0.8568 (t0) REVERT: B 63 LEU cc_start: 0.9226 (tp) cc_final: 0.9003 (tp) REVERT: B 122 TRP cc_start: 0.7558 (p90) cc_final: 0.7208 (p90) REVERT: D 12 LEU cc_start: 0.8965 (mt) cc_final: 0.8627 (mp) REVERT: D 108 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7303 (tptt) REVERT: D 175 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.7800 (tpp80) REVERT: D 200 THR cc_start: 0.7238 (t) cc_final: 0.6907 (t) REVERT: D 201 TYR cc_start: 0.8502 (p90) cc_final: 0.8004 (p90) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3203 time to fit residues: 84.2862 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 129 optimal weight: 0.4980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.079257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.062945 restraints weight = 56356.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065413 restraints weight = 34663.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.067342 restraints weight = 23896.742| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.8021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12304 Z= 0.140 Angle : 0.564 6.480 16923 Z= 0.313 Chirality : 0.039 0.173 1980 Planarity : 0.004 0.071 1878 Dihedral : 20.441 177.728 2326 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.61 (0.23), residues: 1324 helix: 1.25 (0.18), residues: 776 sheet: -0.40 (0.37), residues: 156 loop : -0.84 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 122 HIS 0.002 0.001 HIS B 283 PHE 0.030 0.002 PHE A 23 TYR 0.008 0.001 TYR D 28 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 694) hydrogen bonds : angle 4.59639 ( 1893) covalent geometry : bond 0.00303 (12304) covalent geometry : angle 0.56448 (16923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 MSE cc_start: 0.6405 (mtm) cc_final: 0.5942 (mtp) REVERT: C 122 TRP cc_start: 0.8145 (p90) cc_final: 0.7386 (p90) REVERT: A 108 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7178 (tptt) REVERT: A 135 MSE cc_start: 0.7899 (tpp) cc_final: 0.7213 (tpp) REVERT: A 139 PHE cc_start: 0.8752 (m-80) cc_final: 0.8475 (m-10) REVERT: A 175 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7931 (tpp80) REVERT: A 236 MSE cc_start: 0.4221 (mtp) cc_final: 0.3045 (mtp) REVERT: A 274 TYR cc_start: 0.7679 (m-80) cc_final: 0.7329 (m-80) REVERT: B 59 LYS cc_start: 0.9401 (ttmm) cc_final: 0.9128 (ttmm) REVERT: B 62 ASN cc_start: 0.9243 (m110) cc_final: 0.8739 (t0) REVERT: B 63 LEU cc_start: 0.9254 (tp) cc_final: 0.8903 (tp) REVERT: B 122 TRP cc_start: 0.8132 (p90) cc_final: 0.7421 (p90) REVERT: B 160 MSE cc_start: 0.4619 (ttm) cc_final: 0.3331 (mtp) REVERT: D 108 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7171 (tptt) REVERT: D 175 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.7730 (tpp80) REVERT: D 200 THR cc_start: 0.7081 (t) cc_final: 0.6713 (t) REVERT: D 201 TYR cc_start: 0.8608 (p90) cc_final: 0.8105 (p90) REVERT: D 236 MSE cc_start: 0.3806 (mmm) cc_final: 0.3450 (mtt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2139 time to fit residues: 53.5154 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS B 6 GLN D 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.077642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.061452 restraints weight = 58526.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063787 restraints weight = 36371.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065637 restraints weight = 25224.876| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12304 Z= 0.201 Angle : 0.657 10.085 16923 Z= 0.360 Chirality : 0.041 0.150 1980 Planarity : 0.005 0.076 1878 Dihedral : 20.535 177.848 2326 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.28 (0.23), residues: 1324 helix: 1.03 (0.18), residues: 776 sheet: -0.55 (0.38), residues: 150 loop : -1.07 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 122 HIS 0.005 0.001 HIS B 283 PHE 0.033 0.003 PHE C 171 TYR 0.022 0.002 TYR C 28 ARG 0.004 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 694) hydrogen bonds : angle 5.01386 ( 1893) covalent geometry : bond 0.00434 (12304) covalent geometry : angle 0.65664 (16923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 LEU cc_start: 0.9308 (mm) cc_final: 0.8977 (mm) REVERT: C 19 MSE cc_start: 0.6192 (mtm) cc_final: 0.5976 (mtm) REVERT: C 193 MSE cc_start: 0.6351 (ptm) cc_final: 0.6073 (ptt) REVERT: A 108 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7216 (tptt) REVERT: A 175 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.7912 (tpp80) REVERT: A 236 MSE cc_start: 0.4197 (mtp) cc_final: 0.3904 (mtp) REVERT: A 274 TYR cc_start: 0.7734 (m-80) cc_final: 0.7401 (m-80) REVERT: B 62 ASN cc_start: 0.9215 (m110) cc_final: 0.8718 (t0) REVERT: B 63 LEU cc_start: 0.9105 (tp) cc_final: 0.8768 (tp) REVERT: B 160 MSE cc_start: 0.4788 (ttm) cc_final: 0.3964 (mtp) REVERT: D 12 LEU cc_start: 0.9401 (mp) cc_final: 0.9165 (mp) REVERT: D 108 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7201 (tptt) REVERT: D 139 PHE cc_start: 0.8723 (m-10) cc_final: 0.8371 (m-10) REVERT: D 175 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.7896 (tpp80) REVERT: D 274 TYR cc_start: 0.7978 (m-80) cc_final: 0.7566 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2141 time to fit residues: 51.3107 Evaluate side-chains 133 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.078488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062602 restraints weight = 58048.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.065059 restraints weight = 35192.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.066939 restraints weight = 24239.792| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.8615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12304 Z= 0.149 Angle : 0.597 10.125 16923 Z= 0.328 Chirality : 0.039 0.152 1980 Planarity : 0.004 0.076 1878 Dihedral : 20.446 178.410 2326 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.59 (0.23), residues: 1324 helix: 1.29 (0.18), residues: 764 sheet: -0.55 (0.38), residues: 152 loop : -0.86 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 122 HIS 0.003 0.001 HIS B 283 PHE 0.023 0.002 PHE D 23 TYR 0.009 0.001 TYR A 28 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 694) hydrogen bonds : angle 4.79572 ( 1893) covalent geometry : bond 0.00331 (12304) covalent geometry : angle 0.59701 (16923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 MSE cc_start: 0.6258 (mtm) cc_final: 0.5549 (mtp) REVERT: A 108 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7192 (tptt) REVERT: A 135 MSE cc_start: 0.7748 (tpp) cc_final: 0.7137 (tpp) REVERT: A 139 PHE cc_start: 0.8988 (m-10) cc_final: 0.8332 (m-10) REVERT: A 175 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7822 (tpp80) REVERT: A 236 MSE cc_start: 0.4062 (mtp) cc_final: 0.3371 (mtp) REVERT: A 274 TYR cc_start: 0.7700 (m-80) cc_final: 0.7352 (m-80) REVERT: B 19 MSE cc_start: 0.6902 (mmm) cc_final: 0.6301 (mmm) REVERT: B 62 ASN cc_start: 0.9248 (m110) cc_final: 0.8720 (t0) REVERT: B 63 LEU cc_start: 0.9101 (tp) cc_final: 0.8818 (tp) REVERT: B 122 TRP cc_start: 0.8109 (p90) cc_final: 0.7368 (p90) REVERT: D 108 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7186 (tptt) REVERT: D 111 ILE cc_start: 0.8496 (tp) cc_final: 0.8197 (mt) REVERT: D 175 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.7714 (tpp80) REVERT: D 274 TYR cc_start: 0.7998 (m-80) cc_final: 0.7586 (m-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2119 time to fit residues: 53.8619 Evaluate side-chains 133 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058992 restraints weight = 59468.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061322 restraints weight = 36259.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.063094 restraints weight = 24810.697| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12304 Z= 0.245 Angle : 0.712 13.774 16923 Z= 0.386 Chirality : 0.042 0.196 1980 Planarity : 0.005 0.086 1878 Dihedral : 20.533 177.164 2326 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.01 (0.23), residues: 1324 helix: 0.78 (0.18), residues: 780 sheet: -0.82 (0.38), residues: 148 loop : -1.06 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 122 HIS 0.008 0.002 HIS B 192 PHE 0.033 0.003 PHE A 23 TYR 0.012 0.002 TYR C 273 ARG 0.005 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 694) hydrogen bonds : angle 5.24315 ( 1893) covalent geometry : bond 0.00526 (12304) covalent geometry : angle 0.71203 (16923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.46 seconds wall clock time: 71 minutes 35.40 seconds (4295.40 seconds total)