Starting phenix.real_space_refine on Mon Dec 30 01:29:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3g_18864/12_2024/8r3g_18864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3g_18864/12_2024/8r3g_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_18864/12_2024/8r3g_18864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3g_18864/12_2024/8r3g_18864.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3g_18864/12_2024/8r3g_18864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3g_18864/12_2024/8r3g_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.20, 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: 3.03 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: 5.42 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: 4.69 Time building geometry restraints manager: 3.52 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: 5.160 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: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.780 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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= 0.869 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 *********************** 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 : 1.458 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: 0.2932 time to fit residues: 156.9584 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 : 1.266 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 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= 0.274 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 *********************** 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 : 1.212 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: 0.8816 (mp) cc_final: 0.8152 (mp) REVERT: C 35 ILE cc_start: 0.8212 (mm) cc_final: 0.7996 (mm) REVERT: C 125 LYS cc_start: 0.7828 (mttm) cc_final: 0.7315 (tttt) REVERT: A 145 VAL cc_start: 0.7741 (t) cc_final: 0.7415 (t) REVERT: A 236 MSE cc_start: 0.4309 (mtm) cc_final: 0.3839 (mtm) REVERT: B 71 MSE cc_start: 0.6559 (mpp) cc_final: 0.6018 (mtm) REVERT: B 132 VAL cc_start: 0.8686 (t) cc_final: 0.8066 (p) REVERT: B 156 VAL cc_start: 0.8975 (t) cc_final: 0.8536 (t) REVERT: B 203 LEU cc_start: 0.5708 (mt) cc_final: 0.5311 (mt) REVERT: B 304 VAL cc_start: 0.7995 (t) cc_final: 0.7784 (m) REVERT: D 236 MSE cc_start: 0.4173 (mtm) cc_final: 0.3904 (mtm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2610 time to fit residues: 91.4788 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 : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.5303 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= 0.182 Angle : 0.592 7.674 16923 Z= 0.324 Chirality : 0.041 0.194 1980 Planarity : 0.004 0.068 1878 Dihedral : 20.565 179.740 2326 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.00 (0.23), residues: 1324 helix: 1.35 (0.18), residues: 758 sheet: 0.09 (0.36), residues: 158 loop : -0.27 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 122 HIS 0.002 0.001 HIS B 283 PHE 0.023 0.002 PHE D 271 TYR 0.017 0.002 TYR B 201 ARG 0.003 0.001 ARG A 175 *********************** 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 208 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.187 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 15 LEU cc_start: 0.8666 (mp) cc_final: 0.7997 (mp) REVERT: C 132 VAL cc_start: 0.8494 (t) cc_final: 0.7825 (p) REVERT: C 156 VAL cc_start: 0.9027 (t) cc_final: 0.8724 (t) REVERT: C 203 LEU cc_start: 0.5225 (mt) cc_final: 0.4780 (mt) REVERT: C 247 MSE cc_start: -0.0277 (mmm) cc_final: -0.0609 (mmp) REVERT: A 295 ILE cc_start: 0.8587 (pt) cc_final: 0.8359 (pt) REVERT: B 15 LEU cc_start: 0.8595 (mp) cc_final: 0.7876 (mm) REVERT: B 132 VAL cc_start: 0.8530 (t) cc_final: 0.7813 (p) REVERT: B 156 VAL cc_start: 0.8903 (t) cc_final: 0.8691 (t) REVERT: D 290 MSE cc_start: 0.5345 (mmp) cc_final: 0.4937 (mmt) REVERT: D 295 ILE cc_start: 0.8677 (pt) cc_final: 0.8343 (pt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2406 time to fit residues: 72.1244 Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12304 Z= 0.236 Angle : 0.598 6.850 16923 Z= 0.335 Chirality : 0.040 0.140 1980 Planarity : 0.005 0.062 1878 Dihedral : 20.516 176.887 2326 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 0.86 (0.23), residues: 1324 helix: 1.29 (0.18), residues: 760 sheet: 0.10 (0.36), residues: 154 loop : -0.46 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 122 HIS 0.003 0.001 HIS B 192 PHE 0.021 0.002 PHE D 271 TYR 0.019 0.002 TYR C 201 ARG 0.005 0.001 ARG B 250 *********************** 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 180 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.325 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: C 15 LEU cc_start: 0.8749 (mp) cc_final: 0.8047 (mp) REVERT: C 201 TYR cc_start: 0.4834 (p90) cc_final: 0.4571 (p90) REVERT: B 71 MSE cc_start: 0.6562 (mpp) cc_final: 0.5434 (mtm) REVERT: D 288 VAL cc_start: 0.7801 (m) cc_final: 0.7509 (m) REVERT: D 295 ILE cc_start: 0.8942 (pt) cc_final: 0.8587 (pt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2252 time to fit residues: 61.1673 Evaluate side-chains 137 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 115 optimal weight: 0.0470 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12304 Z= 0.155 Angle : 0.547 7.376 16923 Z= 0.304 Chirality : 0.039 0.136 1980 Planarity : 0.004 0.063 1878 Dihedral : 20.419 179.040 2326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.97 (0.23), residues: 1324 helix: 1.41 (0.18), residues: 758 sheet: 0.28 (0.37), residues: 152 loop : -0.54 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 122 HIS 0.002 0.000 HIS B 283 PHE 0.023 0.002 PHE A 139 TYR 0.019 0.002 TYR C 201 ARG 0.003 0.000 ARG D 175 *********************** 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 191 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.293 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 15 LEU cc_start: 0.8763 (mp) cc_final: 0.7966 (mp) REVERT: C 46 ILE cc_start: 0.7698 (pt) cc_final: 0.7487 (pt) REVERT: C 120 SER cc_start: 0.6559 (p) cc_final: 0.6169 (m) REVERT: A 19 MSE cc_start: 0.4054 (ptm) cc_final: 0.3154 (ptp) REVERT: A 236 MSE cc_start: 0.4155 (mtp) cc_final: 0.3767 (mtp) REVERT: A 295 ILE cc_start: 0.8669 (pt) cc_final: 0.8393 (pt) REVERT: D 88 MSE cc_start: 0.5338 (mtp) cc_final: 0.4821 (ttm) REVERT: D 236 MSE cc_start: 0.3989 (mtp) cc_final: 0.3642 (mtp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2248 time to fit residues: 63.3964 Evaluate side-chains 143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12304 Z= 0.227 Angle : 0.592 10.459 16923 Z= 0.331 Chirality : 0.040 0.140 1980 Planarity : 0.004 0.067 1878 Dihedral : 20.391 177.326 2326 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 0.87 (0.23), residues: 1324 helix: 1.34 (0.19), residues: 764 sheet: -0.00 (0.38), residues: 154 loop : -0.53 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 122 HIS 0.004 0.001 HIS B 192 PHE 0.021 0.002 PHE D 271 TYR 0.010 0.001 TYR A 317 ARG 0.006 0.001 ARG B 250 *********************** 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 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.106 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 120 SER cc_start: 0.6324 (p) cc_final: 0.6080 (m) REVERT: C 122 TRP cc_start: 0.6114 (p90) cc_final: 0.5393 (p90) REVERT: A 295 ILE cc_start: 0.8872 (pt) cc_final: 0.8643 (pt) REVERT: B 120 SER cc_start: 0.5991 (p) cc_final: 0.5533 (m) REVERT: B 132 VAL cc_start: 0.8465 (t) cc_final: 0.7693 (t) REVERT: D 88 MSE cc_start: 0.5876 (mtp) cc_final: 0.5487 (ttm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2070 time to fit residues: 51.8936 Evaluate side-chains 132 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12304 Z= 0.196 Angle : 0.587 9.959 16923 Z= 0.327 Chirality : 0.039 0.155 1980 Planarity : 0.004 0.071 1878 Dihedral : 20.376 178.628 2326 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 0.85 (0.23), residues: 1324 helix: 1.35 (0.19), residues: 762 sheet: 0.10 (0.38), residues: 154 loop : -0.66 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 122 HIS 0.005 0.001 HIS B 192 PHE 0.021 0.002 PHE D 271 TYR 0.013 0.001 TYR C 28 ARG 0.006 0.000 ARG B 250 *********************** 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 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.300 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: C 46 ILE cc_start: 0.7785 (pt) cc_final: 0.7578 (pt) REVERT: C 135 MSE cc_start: 0.2670 (ptp) cc_final: 0.1976 (ptt) REVERT: B 54 GLU cc_start: 0.7665 (mp0) cc_final: 0.7444 (mm-30) REVERT: B 59 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8018 (tppt) REVERT: B 132 VAL cc_start: 0.8689 (t) cc_final: 0.8457 (t) REVERT: D 88 MSE cc_start: 0.5776 (mtp) cc_final: 0.5125 (ttm) REVERT: D 201 TYR cc_start: 0.6897 (p90) cc_final: 0.6652 (p90) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2068 time to fit residues: 52.2143 Evaluate side-chains 132 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.8216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12304 Z= 0.293 Angle : 0.672 7.346 16923 Z= 0.374 Chirality : 0.042 0.151 1980 Planarity : 0.005 0.076 1878 Dihedral : 20.548 177.226 2326 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.35 (0.23), residues: 1324 helix: 0.92 (0.18), residues: 762 sheet: -0.33 (0.38), residues: 150 loop : -0.69 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.006 0.002 HIS B 192 PHE 0.022 0.003 PHE D 271 TYR 0.014 0.002 TYR A 317 ARG 0.007 0.001 ARG B 250 *********************** 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 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MSE cc_start: 0.6647 (tpp) cc_final: 0.6377 (tpt) REVERT: C 132 VAL cc_start: 0.8900 (t) cc_final: 0.8586 (t) REVERT: C 207 PRO cc_start: 0.6520 (Cg_exo) cc_final: 0.6284 (Cg_endo) REVERT: A 295 ILE cc_start: 0.8640 (pt) cc_final: 0.8435 (pt) REVERT: B 19 MSE cc_start: 0.6185 (mtm) cc_final: 0.5733 (mtp) REVERT: B 24 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 59 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8137 (tppt) REVERT: B 88 MSE cc_start: 0.6810 (tpp) cc_final: 0.6328 (tpt) REVERT: D 88 MSE cc_start: 0.6102 (mtp) cc_final: 0.5811 (ttm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2135 time to fit residues: 53.7611 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0470 chunk 125 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.8311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12304 Z= 0.168 Angle : 0.591 7.917 16923 Z= 0.329 Chirality : 0.040 0.153 1980 Planarity : 0.004 0.074 1878 Dihedral : 20.429 179.318 2326 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.54 (0.23), residues: 1324 helix: 1.19 (0.19), residues: 774 sheet: -0.31 (0.37), residues: 156 loop : -0.91 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 122 HIS 0.004 0.001 HIS D 286 PHE 0.026 0.002 PHE D 139 TYR 0.009 0.001 TYR C 28 ARG 0.005 0.000 ARG B 250 *********************** 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 172 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MSE cc_start: 0.2716 (ptp) cc_final: 0.1930 (ptt) REVERT: A 295 ILE cc_start: 0.8663 (pt) cc_final: 0.8432 (pt) REVERT: B 19 MSE cc_start: 0.6202 (mtm) cc_final: 0.5875 (mtp) REVERT: B 88 MSE cc_start: 0.6613 (tpp) cc_final: 0.6174 (tpt) REVERT: B 132 VAL cc_start: 0.8542 (t) cc_final: 0.8211 (t) REVERT: D 295 ILE cc_start: 0.8767 (pt) cc_final: 0.8552 (pt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2161 time to fit residues: 55.3445 Evaluate side-chains 131 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.8896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12304 Z= 0.414 Angle : 0.804 8.977 16923 Z= 0.441 Chirality : 0.045 0.231 1980 Planarity : 0.006 0.089 1878 Dihedral : 20.707 176.703 2326 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.70 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.30 (0.23), residues: 1324 helix: 0.45 (0.18), residues: 776 sheet: -0.43 (0.39), residues: 142 loop : -1.19 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 122 HIS 0.007 0.002 HIS B 283 PHE 0.021 0.004 PHE D 271 TYR 0.017 0.003 TYR B 273 ARG 0.007 0.001 ARG B 52 ********************** 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 153 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MSE cc_start: 0.6823 (tpp) cc_final: 0.6518 (tpt) REVERT: C 189 ILE cc_start: 0.8003 (mp) cc_final: 0.7786 (mp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2012 time to fit residues: 47.3679 Evaluate side-chains 128 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.077293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061650 restraints weight = 58453.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.063964 restraints weight = 35992.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065736 restraints weight = 24961.280| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12304 Z= 0.205 Angle : 0.648 10.933 16923 Z= 0.352 Chirality : 0.041 0.164 1980 Planarity : 0.004 0.076 1878 Dihedral : 20.538 178.952 2326 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.23 (0.23), residues: 1324 helix: 0.98 (0.18), residues: 778 sheet: -0.47 (0.37), residues: 146 loop : -1.14 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 122 HIS 0.003 0.001 HIS B 283 PHE 0.028 0.003 PHE D 139 TYR 0.009 0.001 TYR A 28 ARG 0.006 0.000 ARG B 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.82 seconds wall clock time: 45 minutes 50.57 seconds (2750.57 seconds total)