Starting phenix.real_space_refine on Thu Sep 18 03:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.map" model { file = "/net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kg1_62305/09_2025/9kg1_62305.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8729 2.51 5 N 2387 2.21 5 O 2695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13853 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Chain: "B" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Chain: "D" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Chain: "F" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Chain: "G" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Time building chain proxies: 3.77, per 1000 atoms: 0.27 Number of scatterers: 13853 At special positions: 0 Unit cell: (111.32, 111.32, 86.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2695 8.00 N 2387 7.00 C 8729 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: 1.15 Conformation dependent library (CDL) restraints added in 680.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 39 sheets defined 3.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.619A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.672A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.170A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.640A pdb=" N SER E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 217 through 223 removed outlier: 3.563A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.551A pdb=" N ILE A 61 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.562A pdb=" N LEU A 53 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 232 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.297A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 83 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 157 removed outlier: 4.185A pdb=" N VAL A 169 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 84 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 171 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.555A pdb=" N THR B 230 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.620A pdb=" N ASP B 255 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.525A pdb=" N GLY C 23 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 40 " --> pdb=" O GLY C 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 57 removed outlier: 4.149A pdb=" N PHE C 228 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.802A pdb=" N ARG C 66 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 79 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 78 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.533A pdb=" N LYS C 154 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 156 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AC1, first strand: chain 'D' and resid 27 through 29 removed outlier: 3.600A pdb=" N THR D 27 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 36 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 57 removed outlier: 4.095A pdb=" N PHE D 228 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 155 through 158 removed outlier: 4.303A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 165 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 86 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 84 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 251 " --> pdb=" O ASP D 276 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP D 276 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'D' and resid 256 through 260 Processing sheet with id=AC6, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AC7, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.550A pdb=" N MET E 34 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 54 through 56 removed outlier: 3.545A pdb=" N ASP E 100 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR E 233 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE E 98 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 66 through 69 removed outlier: 6.066A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE E 171 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE E 84 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 86 " --> pdb=" O TRP E 167 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 165 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 168 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 156 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 66 through 69 removed outlier: 6.066A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 66 through 69 removed outlier: 5.914A pdb=" N VAL F 67 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA F 79 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER F 69 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 153 through 158 removed outlier: 4.164A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 86 " --> pdb=" O TRP F 167 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE F 84 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE F 171 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL F 252 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE F 84 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU F 250 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 86 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE F 248 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU F 88 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP F 246 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG F 251 " --> pdb=" O ASP F 276 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 97 through 102 removed outlier: 5.295A pdb=" N ILE F 98 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR F 233 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 175 through 176 removed outlier: 3.709A pdb=" N ASN F 176 " --> pdb=" O TRP F 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 283 through 285 Processing sheet with id=AD7, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AD8, first strand: chain 'G' and resid 53 through 56 removed outlier: 4.743A pdb=" N LEU G 53 " --> pdb=" O ILE G 232 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE G 232 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 68 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE G 84 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 68 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA G 83 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AE3, first strand: chain 'G' and resid 284 through 285 190 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.46: 2412 1.46 - 1.57: 7257 1.57 - 1.69: 1 1.69 - 1.81: 84 Bond restraints: 14161 Sorted by residual: bond pdb=" CB ARG D 184 " pdb=" CG ARG D 184 " ideal model delta sigma weight residual 1.520 1.592 -0.072 3.00e-02 1.11e+03 5.78e+00 bond pdb=" N ASN D 188 " pdb=" CA ASN D 188 " ideal model delta sigma weight residual 1.457 1.427 0.030 1.41e-02 5.03e+03 4.56e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N ALA C 1 " pdb=" CA ALA C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ALA F 1 " pdb=" CA ALA F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 14156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 18115 1.59 - 3.19: 874 3.19 - 4.78: 115 4.78 - 6.37: 17 6.37 - 7.97: 3 Bond angle restraints: 19124 Sorted by residual: angle pdb=" N ASP B 276 " pdb=" CA ASP B 276 " pdb=" C ASP B 276 " ideal model delta sigma weight residual 109.71 101.74 7.97 1.41e+00 5.03e-01 3.19e+01 angle pdb=" N ASP E 276 " pdb=" CA ASP E 276 " pdb=" C ASP E 276 " ideal model delta sigma weight residual 111.81 104.65 7.16 1.44e+00 4.82e-01 2.47e+01 angle pdb=" N GLN B 241 " pdb=" CA GLN B 241 " pdb=" C GLN B 241 " ideal model delta sigma weight residual 110.44 115.70 -5.26 1.20e+00 6.94e-01 1.92e+01 angle pdb=" N ILE G 5 " pdb=" CA ILE G 5 " pdb=" C ILE G 5 " ideal model delta sigma weight residual 112.83 108.69 4.14 9.90e-01 1.02e+00 1.75e+01 angle pdb=" CA ARG E 184 " pdb=" CB ARG E 184 " pdb=" CG ARG E 184 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 ... (remaining 19119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 7713 17.14 - 34.29: 590 34.29 - 51.43: 150 51.43 - 68.57: 35 68.57 - 85.71: 10 Dihedral angle restraints: 8498 sinusoidal: 3535 harmonic: 4963 Sorted by residual: dihedral pdb=" CA ALA D 83 " pdb=" C ALA D 83 " pdb=" N PHE D 84 " pdb=" CA PHE D 84 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TRP E 274 " pdb=" C TRP E 274 " pdb=" N THR E 275 " pdb=" CA THR E 275 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASN F 264 " pdb=" C ASN F 264 " pdb=" N TRP F 265 " pdb=" CA TRP F 265 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 8495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1102 0.030 - 0.061: 617 0.061 - 0.091: 151 0.091 - 0.121: 119 0.121 - 0.152: 27 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CG LEU D 195 " pdb=" CB LEU D 195 " pdb=" CD1 LEU D 195 " pdb=" CD2 LEU D 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA VAL C 252 " pdb=" N VAL C 252 " pdb=" C VAL C 252 " pdb=" CB VAL C 252 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2013 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 184 " -0.161 9.50e-02 1.11e+02 7.26e-02 3.75e+00 pdb=" NE ARG D 184 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG D 184 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG D 184 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 184 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 149 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C VAL D 149 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL D 149 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN D 150 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 190 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C VAL D 190 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL D 190 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR D 191 " 0.009 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 221 2.46 - 3.07: 10908 3.07 - 3.68: 21650 3.68 - 4.29: 32504 4.29 - 4.90: 51487 Nonbonded interactions: 116770 Sorted by model distance: nonbonded pdb=" OH TYR D 65 " pdb=" O LEU D 211 " model vdw 1.845 3.040 nonbonded pdb=" OH TYR B 65 " pdb=" O LEU B 211 " model vdw 1.864 3.040 nonbonded pdb=" OH TYR B 101 " pdb=" OG1 THR C 60 " model vdw 1.902 3.040 nonbonded pdb=" OH TYR G 65 " pdb=" O LEU G 211 " model vdw 1.906 3.040 nonbonded pdb=" O ASP F 183 " pdb=" OG SER F 186 " model vdw 1.930 3.040 ... (remaining 116765 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14161 Z= 0.226 Angle : 0.774 7.968 19124 Z= 0.450 Chirality : 0.045 0.152 2016 Planarity : 0.005 0.073 2450 Dihedral : 13.842 85.712 5278 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.93 % Favored : 83.94 % Rotamer: Outliers : 3.31 % Allowed : 8.38 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.17), residues: 1638 helix: -2.38 (0.82), residues: 36 sheet: -2.81 (0.22), residues: 463 loop : -3.40 (0.15), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 184 TYR 0.012 0.002 TYR E 28 PHE 0.014 0.002 PHE E 171 TRP 0.014 0.001 TRP A 274 HIS 0.006 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00429 (14161) covalent geometry : angle 0.77436 (19124) hydrogen bonds : bond 0.33911 ( 186) hydrogen bonds : angle 14.36921 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 393 time to evaluate : 0.559 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: A 171 PHE cc_start: 0.3214 (t80) cc_final: 0.2991 (t80) REVERT: A 191 TYR cc_start: 0.1607 (m-10) cc_final: 0.0925 (m-10) REVERT: A 197 MET cc_start: 0.3061 (mtp) cc_final: 0.2763 (mmm) REVERT: B 28 TYR cc_start: 0.5216 (t80) cc_final: 0.4841 (t80) REVERT: B 110 LYS cc_start: 0.4449 (tptt) cc_final: 0.3353 (tptp) REVERT: B 266 LYS cc_start: 0.4586 (tttt) cc_final: 0.3870 (tptm) REVERT: B 269 ASN cc_start: 0.3759 (OUTLIER) cc_final: 0.3043 (p0) REVERT: C 61 ILE cc_start: 0.6735 (mp) cc_final: 0.6339 (mp) REVERT: E 65 TYR cc_start: 0.3730 (t80) cc_final: 0.2956 (t80) REVERT: E 110 LYS cc_start: 0.4279 (tptp) cc_final: 0.3830 (tmtm) REVERT: E 265 TRP cc_start: 0.3295 (m-90) cc_final: 0.2609 (t60) REVERT: F 232 ILE cc_start: 0.5165 (pt) cc_final: 0.4943 (pt) REVERT: F 234 MET cc_start: 0.1420 (mmm) cc_final: 0.0876 (tmt) REVERT: G 176 ASN cc_start: 0.4837 (t0) cc_final: 0.4152 (t0) outliers start: 51 outliers final: 9 residues processed: 428 average time/residue: 0.5038 time to fit residues: 237.9140 Evaluate side-chains 255 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain G residue 101 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 176 ASN A 209 ASN A 259 HIS B 48 HIS ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN C 35 HIS C 97 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 177 GLN G 32 ASN G 173 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.303092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.292037 restraints weight = 20174.188| |-----------------------------------------------------------------------------| r_work (start): 0.5089 rms_B_bonded: 1.65 r_work: 0.5026 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4923 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14161 Z= 0.193 Angle : 0.802 10.364 19124 Z= 0.425 Chirality : 0.049 0.175 2016 Planarity : 0.005 0.057 2450 Dihedral : 7.309 48.649 1839 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.66 % Favored : 88.22 % Rotamer: Outliers : 5.39 % Allowed : 18.83 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.17), residues: 1638 helix: -2.31 (0.66), residues: 47 sheet: -2.74 (0.21), residues: 524 loop : -3.07 (0.15), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 66 TYR 0.023 0.002 TYR C 68 PHE 0.022 0.003 PHE D 224 TRP 0.030 0.002 TRP C 80 HIS 0.005 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00403 (14161) covalent geometry : angle 0.80176 (19124) hydrogen bonds : bond 0.04462 ( 186) hydrogen bonds : angle 9.78149 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 0.600 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: A 7 ILE cc_start: 0.4737 (OUTLIER) cc_final: 0.4051 (mm) REVERT: A 271 LYS cc_start: 0.4366 (ttmm) cc_final: 0.3728 (mptt) REVERT: B 28 TYR cc_start: 0.5275 (t80) cc_final: 0.4686 (t80) REVERT: B 110 LYS cc_start: 0.4426 (tptt) cc_final: 0.4184 (tptp) REVERT: B 266 LYS cc_start: 0.4236 (tttt) cc_final: 0.4021 (tptm) REVERT: B 274 TRP cc_start: 0.4269 (OUTLIER) cc_final: 0.3646 (m100) REVERT: D 256 TYR cc_start: 0.2895 (t80) cc_final: 0.2429 (t80) REVERT: E 274 TRP cc_start: 0.4911 (OUTLIER) cc_final: 0.4526 (m-90) REVERT: F 265 TRP cc_start: 0.3066 (m-90) cc_final: 0.1951 (t60) REVERT: F 266 LYS cc_start: 0.3311 (ttmt) cc_final: 0.2804 (tttt) REVERT: G 30 LYS cc_start: 0.5200 (mppt) cc_final: 0.4824 (mptt) REVERT: G 204 MET cc_start: 0.3031 (pmm) cc_final: 0.2490 (pmm) outliers start: 83 outliers final: 26 residues processed: 333 average time/residue: 0.4105 time to fit residues: 154.0722 Evaluate side-chains 256 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 270 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN C 209 ASN C 214 ASN C 264 ASN D 177 GLN D 293 ASN E 194 GLN F 176 ASN F 177 GLN F 209 ASN G 35 HIS G 269 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.301021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.290830 restraints weight = 20109.471| |-----------------------------------------------------------------------------| r_work (start): 0.5074 rms_B_bonded: 1.62 r_work: 0.5017 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4912 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4503 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14161 Z= 0.155 Angle : 0.713 10.753 19124 Z= 0.376 Chirality : 0.046 0.181 2016 Planarity : 0.005 0.050 2450 Dihedral : 6.337 47.059 1825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.17 % Favored : 88.71 % Rotamer: Outliers : 5.52 % Allowed : 21.82 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.18), residues: 1638 helix: -2.56 (0.61), residues: 47 sheet: -2.72 (0.19), residues: 604 loop : -2.81 (0.16), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 253 TYR 0.025 0.002 TYR B 40 PHE 0.019 0.002 PHE F 210 TRP 0.043 0.002 TRP G 80 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00336 (14161) covalent geometry : angle 0.71316 (19124) hydrogen bonds : bond 0.03632 ( 186) hydrogen bonds : angle 8.75770 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 250 time to evaluate : 0.473 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: A 280 GLU cc_start: 0.4194 (tm-30) cc_final: 0.3572 (tm-30) REVERT: B 110 LYS cc_start: 0.4506 (tptt) cc_final: 0.3662 (tptp) REVERT: B 274 TRP cc_start: 0.4273 (OUTLIER) cc_final: 0.3751 (m-10) REVERT: C 46 LYS cc_start: 0.2094 (OUTLIER) cc_final: 0.1117 (mmmt) REVERT: D 110 LYS cc_start: 0.5634 (tptt) cc_final: 0.4635 (tptp) REVERT: D 204 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3196 (mmt) REVERT: D 256 TYR cc_start: 0.2910 (t80) cc_final: 0.2541 (t80) REVERT: E 282 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.3691 (m-80) REVERT: F 110 LYS cc_start: 0.4741 (tptt) cc_final: 0.4443 (tptp) REVERT: F 254 ASP cc_start: 0.4634 (t70) cc_final: 0.4381 (t70) REVERT: F 265 TRP cc_start: 0.3200 (m-90) cc_final: 0.2184 (t60) REVERT: F 266 LYS cc_start: 0.3116 (ttmt) cc_final: 0.2846 (tttt) REVERT: G 30 LYS cc_start: 0.5151 (mppt) cc_final: 0.4937 (mptt) REVERT: G 266 LYS cc_start: 0.4629 (mtpt) cc_final: 0.4410 (mttm) REVERT: G 272 ASP cc_start: 0.4599 (m-30) cc_final: 0.4225 (m-30) REVERT: G 274 TRP cc_start: 0.3732 (m-90) cc_final: 0.3527 (m-90) outliers start: 85 outliers final: 37 residues processed: 303 average time/residue: 0.4308 time to fit residues: 147.2181 Evaluate side-chains 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 270 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 176 ASN ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN F 209 ASN F 242 GLN G 97 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.299250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.289267 restraints weight = 20109.094| |-----------------------------------------------------------------------------| r_work (start): 0.5061 rms_B_bonded: 1.56 r_work: 0.5005 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4898 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4603 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14161 Z= 0.160 Angle : 0.708 10.363 19124 Z= 0.367 Chirality : 0.045 0.169 2016 Planarity : 0.005 0.053 2450 Dihedral : 6.277 49.665 1825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.38 % Favored : 89.50 % Rotamer: Outliers : 5.45 % Allowed : 24.55 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.94 (0.18), residues: 1638 helix: -2.81 (0.44), residues: 71 sheet: -2.52 (0.19), residues: 607 loop : -2.73 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 184 TYR 0.028 0.002 TYR B 40 PHE 0.019 0.002 PHE B 228 TRP 0.049 0.002 TRP A 80 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00352 (14161) covalent geometry : angle 0.70771 (19124) hydrogen bonds : bond 0.03324 ( 186) hydrogen bonds : angle 8.37477 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 219 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TRP cc_start: 0.3881 (t60) cc_final: 0.3434 (t60) REVERT: B 110 LYS cc_start: 0.4597 (tptt) cc_final: 0.3666 (tptp) REVERT: B 266 LYS cc_start: 0.4702 (tptm) cc_final: 0.4424 (tptm) REVERT: B 274 TRP cc_start: 0.4383 (OUTLIER) cc_final: 0.3863 (m-10) REVERT: C 46 LYS cc_start: 0.2191 (OUTLIER) cc_final: 0.1180 (mmmt) REVERT: D 110 LYS cc_start: 0.5547 (tptt) cc_final: 0.4563 (tptp) REVERT: D 197 MET cc_start: 0.3501 (tmm) cc_final: 0.2643 (mmm) REVERT: D 198 LYS cc_start: 0.3545 (OUTLIER) cc_final: 0.2786 (ptmt) REVERT: D 204 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3418 (mtt) REVERT: D 264 ASN cc_start: 0.3616 (p0) cc_final: 0.3138 (p0) REVERT: E 282 TYR cc_start: 0.4097 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: F 110 LYS cc_start: 0.4763 (tptt) cc_final: 0.4310 (tptp) REVERT: F 209 ASN cc_start: 0.3797 (t0) cc_final: 0.3519 (t0) REVERT: G 197 MET cc_start: 0.4899 (pmm) cc_final: 0.4633 (pmm) REVERT: G 266 LYS cc_start: 0.4787 (mtpt) cc_final: 0.4373 (mttm) REVERT: G 272 ASP cc_start: 0.4327 (m-30) cc_final: 0.3920 (m-30) REVERT: G 274 TRP cc_start: 0.4091 (m-90) cc_final: 0.3834 (m-90) REVERT: G 282 TYR cc_start: 0.3374 (OUTLIER) cc_final: 0.2599 (m-80) outliers start: 84 outliers final: 39 residues processed: 276 average time/residue: 0.4184 time to fit residues: 130.4237 Evaluate side-chains 236 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 0.0270 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 209 ASN B 173 ASN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN G 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.296725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.286595 restraints weight = 20403.048| |-----------------------------------------------------------------------------| r_work (start): 0.5026 rms_B_bonded: 1.61 r_work: 0.4970 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4865 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14161 Z= 0.180 Angle : 0.741 11.306 19124 Z= 0.383 Chirality : 0.046 0.176 2016 Planarity : 0.005 0.050 2450 Dihedral : 6.491 51.476 1825 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.74 % Favored : 89.13 % Rotamer: Outliers : 5.78 % Allowed : 25.84 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.18), residues: 1638 helix: -2.44 (0.54), residues: 60 sheet: -2.29 (0.20), residues: 577 loop : -2.77 (0.17), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 184 TYR 0.028 0.002 TYR B 40 PHE 0.022 0.003 PHE B 228 TRP 0.075 0.002 TRP G 80 HIS 0.006 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00400 (14161) covalent geometry : angle 0.74117 (19124) hydrogen bonds : bond 0.03285 ( 186) hydrogen bonds : angle 8.37911 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 216 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4476 (mm) REVERT: A 110 LYS cc_start: 0.4547 (tptt) cc_final: 0.3389 (tptp) REVERT: A 212 ASP cc_start: 0.5588 (t0) cc_final: 0.5056 (m-30) REVERT: B 110 LYS cc_start: 0.4918 (tptt) cc_final: 0.3963 (tptp) REVERT: B 150 GLN cc_start: 0.5711 (OUTLIER) cc_final: 0.5242 (mp10) REVERT: B 251 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.5492 (ptm-80) REVERT: B 274 TRP cc_start: 0.4392 (OUTLIER) cc_final: 0.3895 (m-10) REVERT: C 30 LYS cc_start: 0.5081 (mtpt) cc_final: 0.4856 (mmpt) REVERT: C 46 LYS cc_start: 0.2485 (OUTLIER) cc_final: 0.1118 (mmmt) REVERT: D 110 LYS cc_start: 0.5568 (tptt) cc_final: 0.4531 (tptp) REVERT: D 165 VAL cc_start: 0.6050 (OUTLIER) cc_final: 0.5748 (t) REVERT: D 191 TYR cc_start: 0.2145 (m-10) cc_final: 0.1333 (m-10) REVERT: D 198 LYS cc_start: 0.3256 (OUTLIER) cc_final: 0.2635 (ptmt) REVERT: E 214 ASN cc_start: 0.6925 (m110) cc_final: 0.6643 (m-40) REVERT: F 110 LYS cc_start: 0.4912 (tptt) cc_final: 0.4595 (tptp) REVERT: F 291 MET cc_start: 0.3350 (ptm) cc_final: 0.2747 (ptp) REVERT: G 30 LYS cc_start: 0.4540 (mmpt) cc_final: 0.4007 (mptt) REVERT: G 174 MET cc_start: 0.1908 (OUTLIER) cc_final: -0.0185 (mmt) REVERT: G 266 LYS cc_start: 0.4893 (mtpt) cc_final: 0.4534 (mttm) REVERT: G 274 TRP cc_start: 0.3816 (m-90) cc_final: 0.3497 (m-90) REVERT: G 282 TYR cc_start: 0.3773 (OUTLIER) cc_final: 0.2935 (m-80) outliers start: 89 outliers final: 41 residues processed: 274 average time/residue: 0.4106 time to fit residues: 127.2870 Evaluate side-chains 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 0.0070 chunk 61 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 0.0970 chunk 117 optimal weight: 0.3980 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN B 177 GLN C 176 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.299878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.288566 restraints weight = 20243.891| |-----------------------------------------------------------------------------| r_work (start): 0.5070 rms_B_bonded: 1.66 r_work: 0.5006 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4900 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4632 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14161 Z= 0.123 Angle : 0.663 10.177 19124 Z= 0.342 Chirality : 0.044 0.166 2016 Planarity : 0.004 0.070 2450 Dihedral : 5.928 52.052 1825 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.67 % Favored : 91.21 % Rotamer: Outliers : 4.87 % Allowed : 27.79 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.18), residues: 1638 helix: -2.45 (0.53), residues: 60 sheet: -2.02 (0.21), residues: 550 loop : -2.64 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 253 TYR 0.026 0.002 TYR B 40 PHE 0.014 0.002 PHE F 210 TRP 0.062 0.002 TRP A 80 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00275 (14161) covalent geometry : angle 0.66261 (19124) hydrogen bonds : bond 0.03041 ( 186) hydrogen bonds : angle 7.79287 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.4255 (tptt) cc_final: 0.3148 (tptp) REVERT: A 271 LYS cc_start: 0.3730 (OUTLIER) cc_final: 0.3171 (mptt) REVERT: B 110 LYS cc_start: 0.5040 (tptt) cc_final: 0.3978 (tptp) REVERT: B 274 TRP cc_start: 0.4525 (OUTLIER) cc_final: 0.3874 (m-10) REVERT: C 30 LYS cc_start: 0.4993 (mtpt) cc_final: 0.4749 (mmpt) REVERT: C 46 LYS cc_start: 0.2574 (OUTLIER) cc_final: 0.1326 (mmmt) REVERT: C 176 ASN cc_start: 0.5453 (t0) cc_final: 0.4879 (t0) REVERT: C 191 TYR cc_start: 0.0895 (OUTLIER) cc_final: 0.0606 (m-10) REVERT: C 197 MET cc_start: 0.3841 (ptt) cc_final: 0.3012 (pmt) REVERT: D 110 LYS cc_start: 0.5419 (tptt) cc_final: 0.4430 (tptp) REVERT: D 191 TYR cc_start: 0.1745 (m-10) cc_final: 0.0877 (m-10) REVERT: D 198 LYS cc_start: 0.2784 (OUTLIER) cc_final: 0.2219 (ptmt) REVERT: D 264 ASN cc_start: 0.3905 (p0) cc_final: 0.3343 (p0) REVERT: E 291 MET cc_start: 0.5001 (tpp) cc_final: 0.4785 (mmt) REVERT: F 97 GLN cc_start: 0.4855 (pm20) cc_final: 0.3759 (mt0) REVERT: F 110 LYS cc_start: 0.5199 (tptt) cc_final: 0.4895 (tptp) REVERT: F 234 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2907 (mmp) REVERT: F 254 ASP cc_start: 0.4501 (t70) cc_final: 0.4209 (t70) REVERT: F 291 MET cc_start: 0.3192 (ptm) cc_final: 0.2658 (ptp) REVERT: G 174 MET cc_start: 0.1659 (OUTLIER) cc_final: -0.0624 (mmt) REVERT: G 272 ASP cc_start: 0.4115 (m-30) cc_final: 0.3432 (m-30) REVERT: G 274 TRP cc_start: 0.4188 (m-90) cc_final: 0.3888 (m-90) REVERT: G 282 TYR cc_start: 0.3779 (OUTLIER) cc_final: 0.3242 (m-80) outliers start: 75 outliers final: 36 residues processed: 279 average time/residue: 0.3756 time to fit residues: 118.8627 Evaluate side-chains 238 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 87 GLN ** G 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.297472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.287679 restraints weight = 20098.328| |-----------------------------------------------------------------------------| r_work (start): 0.5053 rms_B_bonded: 1.57 r_work: 0.4986 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4882 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14161 Z= 0.157 Angle : 0.702 10.412 19124 Z= 0.362 Chirality : 0.045 0.172 2016 Planarity : 0.004 0.054 2450 Dihedral : 6.121 53.526 1825 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.38 % Favored : 89.50 % Rotamer: Outliers : 5.32 % Allowed : 27.92 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.18), residues: 1638 helix: -2.42 (0.55), residues: 60 sheet: -2.24 (0.20), residues: 572 loop : -2.58 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 253 TYR 0.024 0.002 TYR A 65 PHE 0.018 0.002 PHE B 228 TRP 0.078 0.002 TRP A 80 HIS 0.011 0.002 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00354 (14161) covalent geometry : angle 0.70213 (19124) hydrogen bonds : bond 0.03212 ( 186) hydrogen bonds : angle 7.81119 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 215 time to evaluate : 0.626 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: A 110 LYS cc_start: 0.4841 (tptt) cc_final: 0.3753 (tptp) REVERT: A 271 LYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3421 (mmtt) REVERT: B 110 LYS cc_start: 0.5000 (tptt) cc_final: 0.4074 (tptp) REVERT: B 150 GLN cc_start: 0.5568 (OUTLIER) cc_final: 0.5150 (mp10) REVERT: B 274 TRP cc_start: 0.4653 (OUTLIER) cc_final: 0.4021 (m-10) REVERT: C 46 LYS cc_start: 0.2564 (OUTLIER) cc_final: 0.1238 (mmmt) REVERT: C 191 TYR cc_start: 0.0972 (OUTLIER) cc_final: 0.0570 (m-10) REVERT: C 274 TRP cc_start: 0.4350 (OUTLIER) cc_final: 0.3171 (m-90) REVERT: D 110 LYS cc_start: 0.5256 (tptt) cc_final: 0.4221 (tptp) REVERT: D 165 VAL cc_start: 0.5930 (OUTLIER) cc_final: 0.5685 (t) REVERT: D 191 TYR cc_start: 0.1821 (m-10) cc_final: 0.0727 (m-10) REVERT: D 198 LYS cc_start: 0.2784 (OUTLIER) cc_final: 0.1900 (ptmt) REVERT: E 291 MET cc_start: 0.4985 (OUTLIER) cc_final: 0.4655 (mmt) REVERT: F 110 LYS cc_start: 0.5286 (tptt) cc_final: 0.4679 (tptp) REVERT: F 291 MET cc_start: 0.3377 (ptm) cc_final: 0.2828 (ptp) REVERT: G 266 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.4599 (tptp) outliers start: 82 outliers final: 40 residues processed: 267 average time/residue: 0.3886 time to fit residues: 118.5893 Evaluate side-chains 249 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 131 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS G 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.298298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.287905 restraints weight = 19908.998| |-----------------------------------------------------------------------------| r_work (start): 0.5046 rms_B_bonded: 1.65 r_work: 0.4989 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4877 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14161 Z= 0.134 Angle : 0.682 10.699 19124 Z= 0.351 Chirality : 0.044 0.248 2016 Planarity : 0.004 0.066 2450 Dihedral : 5.937 53.572 1825 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.36 % Favored : 91.51 % Rotamer: Outliers : 5.00 % Allowed : 28.57 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.18), residues: 1638 helix: -2.29 (0.54), residues: 60 sheet: -2.13 (0.19), residues: 618 loop : -2.58 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 184 TYR 0.023 0.002 TYR A 65 PHE 0.013 0.002 PHE D 153 TRP 0.089 0.002 TRP G 80 HIS 0.007 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00302 (14161) covalent geometry : angle 0.68163 (19124) hydrogen bonds : bond 0.03031 ( 186) hydrogen bonds : angle 7.57490 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 211 time to evaluate : 0.460 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: A 7 ILE cc_start: 0.5007 (OUTLIER) cc_final: 0.4527 (mm) REVERT: A 110 LYS cc_start: 0.4722 (tptt) cc_final: 0.3550 (tptp) REVERT: B 110 LYS cc_start: 0.5048 (tptt) cc_final: 0.4005 (tptp) REVERT: B 150 GLN cc_start: 0.5492 (OUTLIER) cc_final: 0.4955 (mp10) REVERT: B 194 GLN cc_start: 0.4724 (OUTLIER) cc_final: 0.4020 (mp10) REVERT: B 274 TRP cc_start: 0.4468 (OUTLIER) cc_final: 0.3955 (m-10) REVERT: C 46 LYS cc_start: 0.2901 (OUTLIER) cc_final: 0.1427 (mmmt) REVERT: C 274 TRP cc_start: 0.4241 (OUTLIER) cc_final: 0.2992 (m-90) REVERT: D 110 LYS cc_start: 0.5384 (tptt) cc_final: 0.4005 (tptp) REVERT: D 191 TYR cc_start: 0.1512 (m-10) cc_final: 0.0482 (m-10) REVERT: D 198 LYS cc_start: 0.2862 (OUTLIER) cc_final: 0.2034 (ptmt) REVERT: D 264 ASN cc_start: 0.3931 (p0) cc_final: 0.3434 (p0) REVERT: E 27 THR cc_start: 0.4730 (OUTLIER) cc_final: 0.4096 (p) REVERT: E 266 LYS cc_start: 0.4416 (tptt) cc_final: 0.3771 (tptt) REVERT: E 291 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.4634 (mmt) REVERT: F 78 LEU cc_start: 0.6160 (mm) cc_final: 0.5945 (mp) REVERT: F 110 LYS cc_start: 0.5049 (tptt) cc_final: 0.4660 (tptp) REVERT: F 291 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.2857 (ptp) REVERT: G 110 LYS cc_start: 0.4999 (tptp) cc_final: 0.4468 (tptt) REVERT: G 266 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4128 (tmtt) outliers start: 77 outliers final: 45 residues processed: 259 average time/residue: 0.4146 time to fit residues: 121.9369 Evaluate side-chains 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 0.0040 chunk 16 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 63 optimal weight: 10.0000 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN C 177 GLN D 97 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS G 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.299273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.287573 restraints weight = 20046.175| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 1.71 r_work: 0.4991 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4889 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4685 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14161 Z= 0.125 Angle : 0.665 10.095 19124 Z= 0.343 Chirality : 0.044 0.205 2016 Planarity : 0.004 0.058 2450 Dihedral : 5.771 53.633 1825 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.55 % Favored : 91.39 % Rotamer: Outliers : 4.48 % Allowed : 29.35 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.18), residues: 1638 helix: -2.44 (0.55), residues: 55 sheet: -2.00 (0.20), residues: 593 loop : -2.48 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.023 0.002 TYR A 65 PHE 0.014 0.002 PHE D 196 TRP 0.080 0.002 TRP G 80 HIS 0.006 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00282 (14161) covalent geometry : angle 0.66478 (19124) hydrogen bonds : bond 0.02950 ( 186) hydrogen bonds : angle 7.33554 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 0.546 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: A 7 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4536 (mm) REVERT: A 110 LYS cc_start: 0.4900 (tptt) cc_final: 0.3688 (tptp) REVERT: B 110 LYS cc_start: 0.4940 (tptt) cc_final: 0.3973 (tptp) REVERT: B 194 GLN cc_start: 0.4679 (OUTLIER) cc_final: 0.4429 (mp10) REVERT: B 274 TRP cc_start: 0.4432 (OUTLIER) cc_final: 0.3977 (m-10) REVERT: C 46 LYS cc_start: 0.2911 (OUTLIER) cc_final: 0.1430 (mmmt) REVERT: C 291 MET cc_start: 0.4404 (OUTLIER) cc_final: 0.4179 (mtm) REVERT: D 110 LYS cc_start: 0.5404 (tptt) cc_final: 0.5038 (tptt) REVERT: D 191 TYR cc_start: 0.1433 (m-10) cc_final: 0.0386 (m-10) REVERT: D 197 MET cc_start: 0.2636 (tmm) cc_final: 0.2433 (tpt) REVERT: D 198 LYS cc_start: 0.2738 (OUTLIER) cc_final: 0.1910 (ptmt) REVERT: E 27 THR cc_start: 0.4515 (OUTLIER) cc_final: 0.3939 (p) REVERT: E 65 TYR cc_start: 0.4352 (t80) cc_final: 0.3991 (t80) REVERT: E 266 LYS cc_start: 0.4411 (tptt) cc_final: 0.3834 (tptt) REVERT: E 291 MET cc_start: 0.4818 (tpp) cc_final: 0.4528 (mmt) REVERT: F 65 TYR cc_start: 0.4396 (t80) cc_final: 0.2466 (t80) REVERT: F 110 LYS cc_start: 0.4964 (tptt) cc_final: 0.4686 (tptp) REVERT: F 291 MET cc_start: 0.3398 (OUTLIER) cc_final: 0.2789 (ptp) REVERT: G 110 LYS cc_start: 0.5302 (tptp) cc_final: 0.4620 (tptt) REVERT: G 266 LYS cc_start: 0.4996 (OUTLIER) cc_final: 0.4042 (tmtt) outliers start: 69 outliers final: 43 residues processed: 255 average time/residue: 0.4164 time to fit residues: 120.5107 Evaluate side-chains 242 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 266 LYS Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN F 48 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.297071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.286253 restraints weight = 19731.421| |-----------------------------------------------------------------------------| r_work (start): 0.5048 rms_B_bonded: 1.70 r_work: 0.4978 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4657 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14161 Z= 0.140 Angle : 0.697 11.371 19124 Z= 0.360 Chirality : 0.045 0.192 2016 Planarity : 0.005 0.065 2450 Dihedral : 5.903 54.092 1825 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.79 % Favored : 91.15 % Rotamer: Outliers : 4.22 % Allowed : 30.06 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.19), residues: 1638 helix: -2.35 (0.57), residues: 55 sheet: -1.98 (0.20), residues: 592 loop : -2.45 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.023 0.002 TYR A 65 PHE 0.016 0.002 PHE F 171 TRP 0.122 0.002 TRP G 80 HIS 0.007 0.002 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00321 (14161) covalent geometry : angle 0.69730 (19124) hydrogen bonds : bond 0.03103 ( 186) hydrogen bonds : angle 7.42264 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.540 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: A 7 ILE cc_start: 0.4837 (OUTLIER) cc_final: 0.4408 (mm) REVERT: A 110 LYS cc_start: 0.5002 (tptt) cc_final: 0.3740 (tptp) REVERT: B 110 LYS cc_start: 0.4865 (tptt) cc_final: 0.3916 (tptp) REVERT: B 194 GLN cc_start: 0.4875 (OUTLIER) cc_final: 0.4502 (mp10) REVERT: B 220 LEU cc_start: 0.7844 (tp) cc_final: 0.7546 (OUTLIER) REVERT: B 274 TRP cc_start: 0.4597 (OUTLIER) cc_final: 0.4105 (m-10) REVERT: B 275 THR cc_start: 0.6166 (t) cc_final: 0.5777 (m) REVERT: C 46 LYS cc_start: 0.2801 (OUTLIER) cc_final: 0.1398 (mmmt) REVERT: D 40 TYR cc_start: 0.3895 (p90) cc_final: 0.3626 (p90) REVERT: D 191 TYR cc_start: 0.1529 (m-10) cc_final: 0.0418 (m-10) REVERT: D 198 LYS cc_start: 0.2602 (OUTLIER) cc_final: 0.1873 (ptmt) REVERT: D 264 ASN cc_start: 0.3756 (p0) cc_final: 0.3254 (p0) REVERT: E 27 THR cc_start: 0.4544 (OUTLIER) cc_final: 0.3948 (p) REVERT: E 266 LYS cc_start: 0.4442 (tptt) cc_final: 0.3890 (tptt) REVERT: F 110 LYS cc_start: 0.5214 (tptt) cc_final: 0.4974 (tptp) REVERT: F 291 MET cc_start: 0.3330 (ptm) cc_final: 0.2766 (ptp) REVERT: G 266 LYS cc_start: 0.5107 (OUTLIER) cc_final: 0.4099 (tmtt) outliers start: 65 outliers final: 43 residues processed: 245 average time/residue: 0.4153 time to fit residues: 115.7478 Evaluate side-chains 236 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 274 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 266 LYS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS G 193 ASN G 209 ASN ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.295604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.285304 restraints weight = 19941.744| |-----------------------------------------------------------------------------| r_work (start): 0.5023 rms_B_bonded: 1.59 r_work: 0.4958 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4860 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 moved from start: 0.8363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14161 Z= 0.146 Angle : 0.707 11.924 19124 Z= 0.365 Chirality : 0.045 0.217 2016 Planarity : 0.004 0.057 2450 Dihedral : 6.009 54.295 1825 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.35 % Rotamer: Outliers : 4.09 % Allowed : 30.58 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.19), residues: 1638 helix: -2.22 (0.59), residues: 55 sheet: -2.07 (0.20), residues: 605 loop : -2.46 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 184 TYR 0.027 0.002 TYR A 65 PHE 0.015 0.002 PHE B 228 TRP 0.116 0.002 TRP G 80 HIS 0.008 0.002 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00331 (14161) covalent geometry : angle 0.70731 (19124) hydrogen bonds : bond 0.03110 ( 186) hydrogen bonds : angle 7.42007 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4818.66 seconds wall clock time: 83 minutes 11.42 seconds (4991.42 seconds total)