Starting phenix.real_space_refine on Mon Jul 28 21:46:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.map" model { file = "/net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ois_20080/07_2025/6ois_20080.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 62 5.16 5 C 6785 2.51 5 N 1875 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10732 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1016 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1034 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2591 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2583 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 7.03, per 1000 atoms: 0.66 Number of scatterers: 10732 At special positions: 0 Unit cell: (84.53, 96.3, 143.38, 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 62 16.00 O 2010 8.00 N 1875 7.00 C 6785 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 53.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 39 through 58 removed outlier: 3.532A pdb=" N SER A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.697A pdb=" N GLN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.825A pdb=" N ILE A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.886A pdb=" N MET A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 4.152A pdb=" N SER A 154 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 155' Processing helix chain 'B' and resid 40 through 58 removed outlier: 3.503A pdb=" N VAL B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 89 through 103 removed outlier: 3.596A pdb=" N ARG B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.527A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.671A pdb=" N MET B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.771A pdb=" N SER B 154 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 155 " --> pdb=" O TYR B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 155' Processing helix chain 'C' and resid 53 through 99 Processing helix chain 'C' and resid 118 through 125 removed outlier: 4.017A pdb=" N HIS C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.563A pdb=" N VAL C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 157 through 160 No H-bonds generated for 'chain 'C' and resid 157 through 160' Processing helix chain 'C' and resid 165 through 181 removed outlier: 6.687A pdb=" N THR C 178 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 208 through 218 Processing helix chain 'C' and resid 277 through 280 removed outlier: 3.901A pdb=" N LEU C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.611A pdb=" N ASN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 354 through 405 Processing helix chain 'D' and resid 118 through 125 removed outlier: 4.293A pdb=" N HIS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 157 through 160 No H-bonds generated for 'chain 'D' and resid 157 through 160' Processing helix chain 'D' and resid 166 through 181 removed outlier: 6.441A pdb=" N THR D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ARG D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.605A pdb=" N VAL D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 Processing helix chain 'D' and resid 244 through 248 removed outlier: 3.906A pdb=" N ARG D 247 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG D 248 " --> pdb=" O LEU D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 244 through 248' Processing helix chain 'D' and resid 277 through 280 removed outlier: 3.889A pdb=" N LEU D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 280' Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'E' and resid 53 through 98 Processing helix chain 'E' and resid 118 through 125 removed outlier: 4.134A pdb=" N HIS E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 165 through 182 removed outlier: 3.718A pdb=" N SER E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ARG E 179 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.598A pdb=" N VAL E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 244 through 248 removed outlier: 3.716A pdb=" N ARG E 247 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 244 through 248' Processing helix chain 'E' and resid 277 through 280 removed outlier: 3.721A pdb=" N LEU E 280 " --> pdb=" O PRO E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 277 through 280' Processing helix chain 'E' and resid 289 through 299 removed outlier: 3.943A pdb=" N THR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 3.501A pdb=" N MET E 311 " --> pdb=" O THR E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 404 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.294A pdb=" N HIS F 125 " --> pdb=" O GLN F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 157 through 160 No H-bonds generated for 'chain 'F' and resid 157 through 160' Processing helix chain 'F' and resid 166 through 181 removed outlier: 6.441A pdb=" N THR F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ARG F 179 " --> pdb=" O TYR F 175 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 3.605A pdb=" N VAL F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 218 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.906A pdb=" N ARG F 247 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 244 through 248' Processing helix chain 'F' and resid 277 through 280 removed outlier: 3.888A pdb=" N LEU F 280 " --> pdb=" O PRO F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 277 through 280' Processing helix chain 'F' and resid 293 through 299 Processing helix chain 'F' and resid 307 through 313 Processing sheet with id=AA1, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.400A pdb=" N VAL C 304 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 322 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 338 removed outlier: 3.558A pdb=" N LEU C 338 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 185 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.477A pdb=" N VAL D 304 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE D 268 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 302 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.431A pdb=" N VAL E 184 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 7.050A pdb=" N VAL E 304 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE E 268 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 302 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.599A pdb=" N VAL F 185 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AB3, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.477A pdb=" N VAL F 304 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE F 268 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 302 " --> pdb=" O PHE F 268 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1461 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: 3.36 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2676 1.33 - 1.45: 1999 1.45 - 1.57: 6143 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 10916 Sorted by residual: bond pdb=" N ILE E 318 " pdb=" CA ILE E 318 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.22e-02 6.72e+03 1.11e+01 bond pdb=" N THR B 136 " pdb=" CA THR B 136 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.41e-02 5.03e+03 8.86e+00 bond pdb=" N VAL F 237 " pdb=" CA VAL F 237 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.52e+00 bond pdb=" N VAL E 237 " pdb=" CA VAL E 237 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.24e+00 bond pdb=" N LEU B 135 " pdb=" CA LEU B 135 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.64e+00 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 14260 2.61 - 5.22: 409 5.22 - 7.83: 50 7.83 - 10.45: 20 10.45 - 13.06: 1 Bond angle restraints: 14740 Sorted by residual: angle pdb=" N PRO B 137 " pdb=" CA PRO B 137 " pdb=" C PRO B 137 " ideal model delta sigma weight residual 111.38 124.44 -13.06 1.59e+00 3.96e-01 6.74e+01 angle pdb=" N THR A 136 " pdb=" CA THR A 136 " pdb=" C THR A 136 " ideal model delta sigma weight residual 112.35 120.21 -7.86 1.34e+00 5.57e-01 3.44e+01 angle pdb=" N LEU B 135 " pdb=" CA LEU B 135 " pdb=" C LEU B 135 " ideal model delta sigma weight residual 111.14 116.67 -5.53 1.08e+00 8.57e-01 2.62e+01 angle pdb=" C VAL F 237 " pdb=" N GLY F 238 " pdb=" CA GLY F 238 " ideal model delta sigma weight residual 121.35 126.61 -5.26 1.03e+00 9.43e-01 2.61e+01 angle pdb=" N THR B 136 " pdb=" CA THR B 136 " pdb=" C THR B 136 " ideal model delta sigma weight residual 109.81 119.87 -10.06 2.21e+00 2.05e-01 2.07e+01 ... (remaining 14735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 6197 15.22 - 30.44: 319 30.44 - 45.66: 105 45.66 - 60.88: 10 60.88 - 76.10: 5 Dihedral angle restraints: 6636 sinusoidal: 2701 harmonic: 3935 Sorted by residual: dihedral pdb=" CA ASN C 258 " pdb=" C ASN C 258 " pdb=" N GLY C 259 " pdb=" CA GLY C 259 " ideal model delta harmonic sigma weight residual 180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA THR A 136 " pdb=" C THR A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP C 244 " pdb=" C ASP C 244 " pdb=" N LEU C 245 " pdb=" CA LEU C 245 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 6633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1329 0.068 - 0.136: 287 0.136 - 0.204: 41 0.204 - 0.272: 7 0.272 - 0.340: 3 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CA THR B 136 " pdb=" N THR B 136 " pdb=" C THR B 136 " pdb=" CB THR B 136 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO B 137 " pdb=" N PRO B 137 " pdb=" C PRO B 137 " pdb=" CB PRO B 137 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1664 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 234 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" C ARG F 234 " 0.089 2.00e-02 2.50e+03 pdb=" O ARG F 234 " -0.034 2.00e-02 2.50e+03 pdb=" N PRO F 235 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 234 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG D 234 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 235 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 234 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG C 234 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG C 234 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO C 235 " 0.021 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3271 2.83 - 3.35: 10026 3.35 - 3.87: 17028 3.87 - 4.38: 19296 4.38 - 4.90: 33141 Nonbonded interactions: 82762 Sorted by model distance: nonbonded pdb=" ND2 ASN A 93 " pdb=" O PHE A 155 " model vdw 2.315 3.120 nonbonded pdb=" O LEU C 135 " pdb=" OG1 THR C 138 " model vdw 2.317 3.040 nonbonded pdb=" NH2 ARG A 47 " pdb=" OE1 GLN C 80 " model vdw 2.327 3.120 nonbonded pdb=" O ALA B 122 " pdb=" OG1 THR B 125 " model vdw 2.346 3.040 nonbonded pdb=" NE2 HIS D 240 " pdb=" OE2 GLU D 292 " model vdw 2.350 3.120 ... (remaining 82757 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' and resid 39 through 161) } ncs_group { reference = (chain 'C' and (resid 52 through 98 or resid 117 through 405)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.150 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.440 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.009 0.078 10916 Z= 0.383 Angle : 1.051 13.058 14740 Z= 0.572 Chirality : 0.060 0.340 1667 Planarity : 0.007 0.065 1905 Dihedral : 10.801 76.103 4102 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.68 % Allowed : 4.32 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 1341 helix: -1.40 (0.17), residues: 649 sheet: -1.78 (0.75), residues: 40 loop : -1.80 (0.19), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 127 HIS 0.019 0.004 HIS B 118 PHE 0.029 0.004 PHE C 299 TYR 0.025 0.003 TYR E 288 ARG 0.013 0.001 ARG F 331 Details of bonding type rmsd hydrogen bonds : bond 0.15078 ( 498) hydrogen bonds : angle 6.76993 ( 1461) covalent geometry : bond 0.00881 (10916) covalent geometry : angle 1.05103 (14740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: B 49 GLU cc_start: 0.8073 (tt0) cc_final: 0.7807 (tt0) REVERT: C 357 MET cc_start: 0.7518 (mpm) cc_final: 0.7210 (mpm) REVERT: D 193 THR cc_start: 0.9013 (p) cc_final: 0.8807 (p) REVERT: E 151 LYS cc_start: 0.8013 (tmtm) cc_final: 0.7097 (mptt) REVERT: E 199 ASP cc_start: 0.5846 (t0) cc_final: 0.5142 (p0) REVERT: E 311 MET cc_start: 0.9238 (ttp) cc_final: 0.8990 (ttm) outliers start: 8 outliers final: 1 residues processed: 273 average time/residue: 0.3937 time to fit residues: 136.5464 Evaluate side-chains 135 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 133 HIS B 118 HIS B 133 HIS C 92 GLN C 297 ASN C 340 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 345 ASN E 52 ASN E 125 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 297 ASN E 340 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS F 239 GLN F 297 ASN F 345 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096193 restraints weight = 19390.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096975 restraints weight = 13465.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097427 restraints weight = 11029.019| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10916 Z= 0.193 Angle : 0.654 8.663 14740 Z= 0.340 Chirality : 0.044 0.168 1667 Planarity : 0.005 0.045 1905 Dihedral : 5.153 25.288 1478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.64 % Allowed : 8.64 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1341 helix: 0.84 (0.20), residues: 643 sheet: -1.01 (0.83), residues: 40 loop : -1.25 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 372 HIS 0.005 0.001 HIS F 201 PHE 0.021 0.002 PHE C 225 TYR 0.015 0.002 TYR E 189 ARG 0.006 0.001 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.05145 ( 498) hydrogen bonds : angle 4.79382 ( 1461) covalent geometry : bond 0.00454 (10916) covalent geometry : angle 0.65439 (14740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: B 113 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8696 (tp) REVERT: C 237 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8361 (p) REVERT: C 311 MET cc_start: 0.8668 (ttp) cc_final: 0.8464 (ttt) REVERT: C 357 MET cc_start: 0.7417 (mpm) cc_final: 0.7152 (mpm) REVERT: E 151 LYS cc_start: 0.8069 (tmtm) cc_final: 0.7111 (mmtt) REVERT: E 199 ASP cc_start: 0.5574 (t0) cc_final: 0.5050 (p0) REVERT: F 181 MET cc_start: 0.9170 (tpt) cc_final: 0.8911 (tpt) outliers start: 43 outliers final: 22 residues processed: 178 average time/residue: 0.2329 time to fit residues: 59.8657 Evaluate side-chains 142 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS C 92 GLN C 240 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 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 = 0.3724 r_free = 0.3724 target = 0.122420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094807 restraints weight = 19691.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095219 restraints weight = 13192.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095912 restraints weight = 11697.766| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10916 Z= 0.186 Angle : 0.603 7.323 14740 Z= 0.313 Chirality : 0.043 0.216 1667 Planarity : 0.004 0.042 1905 Dihedral : 4.854 25.968 1478 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.22 % Allowed : 10.92 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1341 helix: 1.74 (0.21), residues: 631 sheet: -1.08 (0.85), residues: 40 loop : -0.96 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 372 HIS 0.006 0.001 HIS B 89 PHE 0.016 0.002 PHE C 225 TYR 0.013 0.002 TYR D 279 ARG 0.005 0.001 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 498) hydrogen bonds : angle 4.47019 ( 1461) covalent geometry : bond 0.00444 (10916) covalent geometry : angle 0.60299 (14740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.186 Fit side-chains REVERT: D 297 ASN cc_start: 0.7979 (m110) cc_final: 0.7762 (m-40) REVERT: E 151 LYS cc_start: 0.8075 (tmtm) cc_final: 0.7076 (mmtt) REVERT: E 199 ASP cc_start: 0.5799 (t0) cc_final: 0.5113 (p0) REVERT: E 204 ILE cc_start: 0.7011 (mp) cc_final: 0.6656 (pt) REVERT: E 258 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7796 (p0) REVERT: F 226 ASP cc_start: 0.7285 (m-30) cc_final: 0.6848 (m-30) outliers start: 38 outliers final: 25 residues processed: 152 average time/residue: 0.2096 time to fit residues: 46.9087 Evaluate side-chains 138 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095364 restraints weight = 19371.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096097 restraints weight = 13603.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096725 restraints weight = 11724.314| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10916 Z= 0.151 Angle : 0.568 9.015 14740 Z= 0.291 Chirality : 0.042 0.172 1667 Planarity : 0.004 0.037 1905 Dihedral : 4.677 25.901 1478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.39 % Allowed : 12.02 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1341 helix: 2.02 (0.21), residues: 643 sheet: -1.24 (1.06), residues: 20 loop : -0.85 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.015 0.002 PHE C 225 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 498) hydrogen bonds : angle 4.25551 ( 1461) covalent geometry : bond 0.00360 (10916) covalent geometry : angle 0.56766 (14740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.401 Fit side-chains REVERT: A 130 GLU cc_start: 0.8710 (tp30) cc_final: 0.8493 (tp30) REVERT: B 114 ASP cc_start: 0.8036 (m-30) cc_final: 0.7754 (m-30) REVERT: D 297 ASN cc_start: 0.7966 (m110) cc_final: 0.7749 (m-40) REVERT: E 151 LYS cc_start: 0.8047 (tmtm) cc_final: 0.7012 (mmtt) REVERT: E 199 ASP cc_start: 0.5942 (t0) cc_final: 0.5297 (p0) REVERT: E 204 ILE cc_start: 0.6911 (mp) cc_final: 0.6661 (pt) REVERT: F 196 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7489 (tp30) REVERT: F 226 ASP cc_start: 0.7082 (m-30) cc_final: 0.6592 (m-30) outliers start: 40 outliers final: 25 residues processed: 149 average time/residue: 0.2715 time to fit residues: 60.0531 Evaluate side-chains 139 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095988 restraints weight = 19328.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096097 restraints weight = 13162.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096767 restraints weight = 11212.495| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10916 Z= 0.132 Angle : 0.544 8.947 14740 Z= 0.277 Chirality : 0.041 0.176 1667 Planarity : 0.004 0.038 1905 Dihedral : 4.451 24.518 1477 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.39 % Allowed : 12.45 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1341 helix: 2.26 (0.21), residues: 643 sheet: -1.54 (1.02), residues: 20 loop : -0.68 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.014 0.001 TYR B 51 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 498) hydrogen bonds : angle 4.10816 ( 1461) covalent geometry : bond 0.00314 (10916) covalent geometry : angle 0.54365 (14740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 1.293 Fit side-chains REVERT: A 130 GLU cc_start: 0.8708 (tp30) cc_final: 0.8388 (tp30) REVERT: D 297 ASN cc_start: 0.7884 (m110) cc_final: 0.7666 (m-40) REVERT: E 151 LYS cc_start: 0.8057 (tmtm) cc_final: 0.6991 (mmtt) REVERT: E 199 ASP cc_start: 0.6116 (t0) cc_final: 0.5385 (p0) REVERT: F 196 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7520 (tp30) outliers start: 40 outliers final: 27 residues processed: 152 average time/residue: 0.2251 time to fit residues: 50.1391 Evaluate side-chains 142 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.098167 restraints weight = 19404.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098640 restraints weight = 13429.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099218 restraints weight = 12094.605| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10916 Z= 0.103 Angle : 0.524 9.184 14740 Z= 0.265 Chirality : 0.040 0.183 1667 Planarity : 0.003 0.041 1905 Dihedral : 4.254 24.115 1477 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.96 % Allowed : 13.38 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1341 helix: 2.31 (0.21), residues: 655 sheet: -1.63 (0.95), residues: 20 loop : -0.65 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.023 0.001 TYR B 51 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 498) hydrogen bonds : angle 3.94589 ( 1461) covalent geometry : bond 0.00229 (10916) covalent geometry : angle 0.52394 (14740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8660 (tp30) cc_final: 0.8289 (tp30) REVERT: A 159 ILE cc_start: 0.8631 (pt) cc_final: 0.8305 (pt) REVERT: E 151 LYS cc_start: 0.8039 (tmtm) cc_final: 0.6999 (mmtt) REVERT: E 199 ASP cc_start: 0.6010 (t0) cc_final: 0.5366 (p0) REVERT: F 196 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7413 (tp30) REVERT: F 260 GLU cc_start: 0.7410 (pm20) cc_final: 0.7117 (mp0) outliers start: 35 outliers final: 28 residues processed: 153 average time/residue: 0.2104 time to fit residues: 46.6649 Evaluate side-chains 143 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096578 restraints weight = 19429.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099201 restraints weight = 12080.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100941 restraints weight = 9193.908| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10916 Z= 0.123 Angle : 0.540 9.974 14740 Z= 0.272 Chirality : 0.041 0.185 1667 Planarity : 0.004 0.038 1905 Dihedral : 4.235 23.759 1477 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.22 % Allowed : 14.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1341 helix: 2.43 (0.21), residues: 647 sheet: -1.62 (0.95), residues: 20 loop : -0.58 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.014 0.001 PHE C 225 TYR 0.024 0.001 TYR B 51 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 498) hydrogen bonds : angle 3.91713 ( 1461) covalent geometry : bond 0.00291 (10916) covalent geometry : angle 0.54009 (14740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: D 166 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6993 (tm-30) REVERT: D 195 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8351 (tt) REVERT: E 151 LYS cc_start: 0.8026 (tmtm) cc_final: 0.6981 (mmtt) REVERT: E 199 ASP cc_start: 0.6077 (t0) cc_final: 0.5436 (p0) REVERT: F 260 GLU cc_start: 0.7495 (pm20) cc_final: 0.7207 (mp0) outliers start: 38 outliers final: 29 residues processed: 152 average time/residue: 0.2087 time to fit residues: 46.4271 Evaluate side-chains 144 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 211 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097952 restraints weight = 19056.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100555 restraints weight = 11995.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102303 restraints weight = 9159.122| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10916 Z= 0.102 Angle : 0.530 10.503 14740 Z= 0.266 Chirality : 0.040 0.187 1667 Planarity : 0.003 0.039 1905 Dihedral : 4.104 22.878 1477 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 14.73 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1341 helix: 2.43 (0.21), residues: 657 sheet: -1.82 (0.90), residues: 20 loop : -0.50 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.023 0.001 TYR B 51 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 498) hydrogen bonds : angle 3.80107 ( 1461) covalent geometry : bond 0.00231 (10916) covalent geometry : angle 0.53017 (14740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.8628 (pt) cc_final: 0.8297 (pt) REVERT: D 195 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8362 (tt) REVERT: D 272 MET cc_start: 0.7583 (mmp) cc_final: 0.7146 (mmp) REVERT: E 151 LYS cc_start: 0.8023 (tmtm) cc_final: 0.6973 (mmtt) REVERT: E 199 ASP cc_start: 0.5994 (t0) cc_final: 0.5422 (p0) REVERT: F 181 MET cc_start: 0.8994 (tpt) cc_final: 0.8749 (tpt) outliers start: 31 outliers final: 24 residues processed: 149 average time/residue: 0.2220 time to fit residues: 48.6590 Evaluate side-chains 142 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 127 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 139 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098863 restraints weight = 19533.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099577 restraints weight = 13777.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099924 restraints weight = 11579.175| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10916 Z= 0.107 Angle : 0.545 11.236 14740 Z= 0.273 Chirality : 0.041 0.186 1667 Planarity : 0.004 0.038 1905 Dihedral : 4.078 22.397 1477 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 14.99 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1341 helix: 2.42 (0.21), residues: 658 sheet: -1.80 (0.91), residues: 20 loop : -0.47 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.021 0.001 TYR B 51 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 498) hydrogen bonds : angle 3.79374 ( 1461) covalent geometry : bond 0.00247 (10916) covalent geometry : angle 0.54454 (14740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7888 (tptm) cc_final: 0.7679 (tptm) REVERT: D 195 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8365 (tt) REVERT: D 272 MET cc_start: 0.7595 (mmp) cc_final: 0.7216 (mmp) REVERT: E 151 LYS cc_start: 0.8041 (tmtm) cc_final: 0.7027 (mmtt) REVERT: E 199 ASP cc_start: 0.5981 (t0) cc_final: 0.5453 (p0) REVERT: F 181 MET cc_start: 0.8991 (tpt) cc_final: 0.8776 (tpt) REVERT: F 196 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7422 (tp30) REVERT: F 338 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8800 (pp) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.2546 time to fit residues: 55.6452 Evaluate side-chains 145 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098390 restraints weight = 19315.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099511 restraints weight = 12060.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099239 restraints weight = 11367.383| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10916 Z= 0.101 Angle : 0.551 10.814 14740 Z= 0.275 Chirality : 0.040 0.191 1667 Planarity : 0.003 0.045 1905 Dihedral : 3.996 21.504 1477 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 15.66 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1341 helix: 2.44 (0.21), residues: 659 sheet: -1.91 (0.88), residues: 20 loop : -0.39 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.022 0.001 TYR B 51 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 498) hydrogen bonds : angle 3.72971 ( 1461) covalent geometry : bond 0.00230 (10916) covalent geometry : angle 0.55100 (14740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7854 (tptm) cc_final: 0.7645 (tptm) REVERT: A 159 ILE cc_start: 0.8590 (pt) cc_final: 0.8268 (pt) REVERT: D 195 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8407 (tt) REVERT: D 272 MET cc_start: 0.7577 (mmp) cc_final: 0.7339 (mmp) REVERT: E 151 LYS cc_start: 0.8099 (tmtm) cc_final: 0.7049 (mmtt) REVERT: E 199 ASP cc_start: 0.6129 (t0) cc_final: 0.5446 (p0) REVERT: F 196 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7588 (tp30) REVERT: F 338 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8784 (pp) outliers start: 26 outliers final: 22 residues processed: 147 average time/residue: 0.2249 time to fit residues: 47.5038 Evaluate side-chains 142 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098885 restraints weight = 19181.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099319 restraints weight = 14043.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099698 restraints weight = 12146.755| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10916 Z= 0.114 Angle : 0.552 10.397 14740 Z= 0.274 Chirality : 0.041 0.187 1667 Planarity : 0.003 0.041 1905 Dihedral : 4.014 21.728 1477 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.37 % Allowed : 15.58 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1341 helix: 2.56 (0.21), residues: 648 sheet: -1.87 (0.92), residues: 20 loop : -0.38 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.005 0.001 HIS A 139 PHE 0.013 0.001 PHE C 225 TYR 0.028 0.001 TYR B 51 ARG 0.009 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 498) hydrogen bonds : angle 3.73354 ( 1461) covalent geometry : bond 0.00270 (10916) covalent geometry : angle 0.55243 (14740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.82 seconds wall clock time: 59 minutes 54.45 seconds (3594.45 seconds total)