Starting phenix.real_space_refine on Fri Feb 14 22:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ois_20080/02_2025/6ois_20080.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ois_20080/02_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_20080/02_2025/6ois_20080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ois_20080/02_2025/6ois_20080.map" model { file = "/net/cci-nas-00/data/ceres_data/6ois_20080/02_2025/6ois_20080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ois_20080/02_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-5592/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: 6.99, per 1000 atoms: 0.65 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: 2.56 Conformation dependent library (CDL) restraints added in 1.4 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: 1.15 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: 3.08 Time building geometry restraints manager: 2.95 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: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.270 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- 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= 0.572 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 *********************** 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 : 1.326 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: 0.3581 time to fit residues: 123.4951 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 : 1.346 ------------------------------------------------------------------------------- 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 = 0.096199 restraints weight = 19390.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096983 restraints weight = 13463.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097435 restraints weight = 11022.747| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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= 0.297 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 *********************** 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 : 1.326 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: 0.8667 (ttp) cc_final: 0.8464 (ttt) REVERT: C 357 MET cc_start: 0.7417 (mpm) cc_final: 0.7153 (mpm) REVERT: E 151 LYS cc_start: 0.8068 (tmtm) cc_final: 0.7111 (mmtt) REVERT: E 199 ASP cc_start: 0.5572 (t0) cc_final: 0.5050 (p0) REVERT: F 181 MET cc_start: 0.9171 (tpt) cc_final: 0.8912 (tpt) outliers start: 43 outliers final: 22 residues processed: 178 average time/residue: 0.2264 time to fit residues: 57.9249 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 : 1.298 ------------------------------------------------------------------------------- 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: 5.9990 chunk 76 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS C 240 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096713 restraints weight = 19557.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097864 restraints weight = 13150.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097648 restraints weight = 11201.043| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10916 Z= 0.205 Angle : 0.566 7.516 14740 Z= 0.291 Chirality : 0.042 0.197 1667 Planarity : 0.004 0.043 1905 Dihedral : 4.742 24.605 1478 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.13 % Allowed : 10.58 % Favored : 86.28 % 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: 0.53 (0.23), residues: 1341 helix: 1.66 (0.21), residues: 648 sheet: -1.04 (0.85), residues: 40 loop : -0.92 (0.22), residues: 653 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 D 296 ARG 0.004 0.000 ARG B 64 *********************** 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 163 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.231 Fit side-chains REVERT: A 100 ASP cc_start: 0.8174 (t0) cc_final: 0.7964 (t0) REVERT: A 159 ILE cc_start: 0.8711 (pt) cc_final: 0.8382 (pt) REVERT: C 357 MET cc_start: 0.7228 (mpm) cc_final: 0.6562 (mpp) REVERT: D 297 ASN cc_start: 0.7957 (m110) cc_final: 0.7718 (m-40) REVERT: E 151 LYS cc_start: 0.8079 (tmtm) cc_final: 0.7083 (mmtt) REVERT: E 199 ASP cc_start: 0.5730 (t0) cc_final: 0.5098 (p0) REVERT: E 258 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8025 (p0) REVERT: F 226 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6835 (m-30) outliers start: 37 outliers final: 20 residues processed: 155 average time/residue: 0.2081 time to fit residues: 47.3824 Evaluate side-chains 141 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ASP 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: 10.0000 chunk 114 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095256 restraints weight = 19377.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096363 restraints weight = 13127.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096423 restraints weight = 11256.895| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10916 Z= 0.249 Angle : 0.569 9.740 14740 Z= 0.291 Chirality : 0.042 0.174 1667 Planarity : 0.004 0.036 1905 Dihedral : 4.578 25.786 1477 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.22 % Allowed : 11.52 % Favored : 85.27 % 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: 0.90 (0.23), residues: 1341 helix: 2.07 (0.21), residues: 645 sheet: -1.15 (1.07), residues: 20 loop : -0.84 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.005 0.001 HIS E 240 PHE 0.015 0.002 PHE C 225 TYR 0.014 0.001 TYR B 51 ARG 0.006 0.000 ARG B 134 *********************** 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 164 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.197 Fit side-chains REVERT: A 130 GLU cc_start: 0.8682 (tp30) cc_final: 0.8389 (tp30) REVERT: C 357 MET cc_start: 0.7103 (mpm) cc_final: 0.6461 (mpp) REVERT: D 297 ASN cc_start: 0.7986 (m110) cc_final: 0.7764 (m-40) REVERT: E 151 LYS cc_start: 0.8060 (tmtm) cc_final: 0.7037 (mmtt) REVERT: E 199 ASP cc_start: 0.5831 (t0) cc_final: 0.5156 (p0) REVERT: E 204 ILE cc_start: 0.6866 (mp) cc_final: 0.6613 (pt) REVERT: E 258 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7894 (p0) REVERT: F 226 ASP cc_start: 0.7074 (m-30) cc_final: 0.6627 (m-30) outliers start: 38 outliers final: 24 residues processed: 154 average time/residue: 0.2090 time to fit residues: 47.5006 Evaluate side-chains 141 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 159 ILE 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094871 restraints weight = 19406.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095949 restraints weight = 13038.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095913 restraints weight = 12740.674| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10916 Z= 0.257 Angle : 0.562 8.119 14740 Z= 0.289 Chirality : 0.042 0.178 1667 Planarity : 0.004 0.050 1905 Dihedral : 4.515 25.723 1477 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.64 % Allowed : 12.11 % Favored : 84.25 % 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: 1.18 (0.23), residues: 1341 helix: 2.39 (0.21), residues: 629 sheet: -1.46 (1.04), residues: 20 loop : -0.70 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.005 0.001 HIS B 89 PHE 0.014 0.002 PHE C 225 TYR 0.013 0.001 TYR B 51 ARG 0.006 0.000 ARG C 347 *********************** 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 164 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 1.353 Fit side-chains REVERT: A 130 GLU cc_start: 0.8743 (tp30) cc_final: 0.8380 (tp30) REVERT: C 255 LYS cc_start: 0.6545 (tptp) cc_final: 0.6234 (tptt) REVERT: C 357 MET cc_start: 0.6990 (mpm) cc_final: 0.6444 (mpp) REVERT: E 151 LYS cc_start: 0.8064 (tmtm) cc_final: 0.7003 (mmtt) REVERT: E 199 ASP cc_start: 0.6053 (t0) cc_final: 0.5354 (p0) REVERT: E 204 ILE cc_start: 0.7001 (mp) cc_final: 0.6729 (pt) outliers start: 43 outliers final: 26 residues processed: 153 average time/residue: 0.2120 time to fit residues: 47.4775 Evaluate side-chains 143 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 193 THR 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 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 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: 1.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.0370 chunk 16 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098323 restraints weight = 19372.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098227 restraints weight = 12684.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098426 restraints weight = 11357.292| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10916 Z= 0.136 Angle : 0.510 9.064 14740 Z= 0.259 Chirality : 0.040 0.180 1667 Planarity : 0.003 0.041 1905 Dihedral : 4.238 23.377 1477 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 13.63 % Favored : 83.74 % 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: 1.35 (0.24), residues: 1341 helix: 2.46 (0.21), residues: 643 sheet: -1.64 (0.97), residues: 20 loop : -0.59 (0.23), residues: 678 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 0.012 0.001 PHE C 225 TYR 0.022 0.001 TYR B 51 ARG 0.002 0.000 ARG D 347 *********************** 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 158 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.046 Fit side-chains REVERT: A 130 GLU cc_start: 0.8619 (tp30) cc_final: 0.8209 (tp30) REVERT: A 159 ILE cc_start: 0.8619 (pt) cc_final: 0.8310 (pt) REVERT: D 166 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6928 (tm-30) REVERT: D 195 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8338 (tt) REVERT: E 151 LYS cc_start: 0.8075 (tmtm) cc_final: 0.6996 (mmtt) REVERT: E 199 ASP cc_start: 0.6095 (t0) cc_final: 0.5513 (p0) REVERT: F 181 MET cc_start: 0.8996 (tpt) cc_final: 0.8790 (tpt) REVERT: F 260 GLU cc_start: 0.7418 (pm20) cc_final: 0.7114 (mp0) outliers start: 31 outliers final: 20 residues processed: 153 average time/residue: 0.2168 time to fit residues: 48.5892 Evaluate side-chains 140 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain C residue 200 ASN 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 195 LEU Chi-restraints excluded: chain D residue 329 ILE 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 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 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: 3.9990 chunk 125 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** 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 = 0.3799 r_free = 0.3799 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099291 restraints weight = 19386.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100279 restraints weight = 11864.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101283 restraints weight = 10384.298| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10916 Z= 0.146 Angle : 0.524 10.257 14740 Z= 0.263 Chirality : 0.040 0.183 1667 Planarity : 0.003 0.039 1905 Dihedral : 4.133 23.277 1477 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.54 % Allowed : 14.56 % Favored : 82.90 % 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: 1.38 (0.24), residues: 1341 helix: 2.39 (0.21), residues: 657 sheet: -1.61 (0.93), residues: 20 loop : -0.54 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 146 HIS 0.004 0.001 HIS E 70 PHE 0.012 0.001 PHE C 225 TYR 0.022 0.001 TYR B 51 ARG 0.002 0.000 ARG B 134 *********************** 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 152 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.223 Fit side-chains REVERT: A 56 LYS cc_start: 0.8070 (tptm) cc_final: 0.7833 (tptm) REVERT: C 181 MET cc_start: 0.9118 (mmm) cc_final: 0.8897 (tpt) REVERT: D 195 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8369 (tt) REVERT: D 272 MET cc_start: 0.7662 (mmp) cc_final: 0.7233 (mmp) REVERT: E 151 LYS cc_start: 0.8087 (tmtm) cc_final: 0.6975 (mmtt) REVERT: E 199 ASP cc_start: 0.6223 (t0) cc_final: 0.5509 (p0) REVERT: F 181 MET cc_start: 0.9078 (tpt) cc_final: 0.8773 (tpt) REVERT: F 196 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7637 (tp30) REVERT: F 260 GLU cc_start: 0.7730 (pm20) cc_final: 0.7415 (mp0) outliers start: 30 outliers final: 22 residues processed: 145 average time/residue: 0.2245 time to fit residues: 46.7398 Evaluate side-chains 143 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 160 PHE 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 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 329 ILE 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 237 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.127611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100087 restraints weight = 19112.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100766 restraints weight = 13463.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101737 restraints weight = 10955.856| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10916 Z= 0.155 Angle : 0.535 10.427 14740 Z= 0.267 Chirality : 0.040 0.186 1667 Planarity : 0.003 0.039 1905 Dihedral : 4.077 22.488 1477 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.20 % Allowed : 14.82 % Favored : 82.98 % 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: 2.63 (0.21), residues: 642 sheet: -1.65 (0.90), residues: 20 loop : -0.45 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.026 0.001 TYR B 51 ARG 0.003 0.000 ARG B 98 *********************** 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 152 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.208 Fit side-chains REVERT: A 56 LYS cc_start: 0.7993 (tptm) cc_final: 0.7768 (tptm) REVERT: C 181 MET cc_start: 0.9072 (mmm) cc_final: 0.8829 (tpt) REVERT: C 272 MET cc_start: 0.8877 (mtt) cc_final: 0.8496 (mtt) REVERT: D 195 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8335 (tt) REVERT: D 272 MET cc_start: 0.7616 (mmp) cc_final: 0.7170 (mmp) REVERT: E 151 LYS cc_start: 0.8016 (tmtm) cc_final: 0.6996 (mmtt) REVERT: E 199 ASP cc_start: 0.6159 (t0) cc_final: 0.5574 (p0) REVERT: F 181 MET cc_start: 0.9041 (tpt) cc_final: 0.8769 (tpt) REVERT: F 196 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7586 (tp30) REVERT: F 260 GLU cc_start: 0.7600 (pm20) cc_final: 0.7335 (mp0) outliers start: 26 outliers final: 22 residues processed: 145 average time/residue: 0.2304 time to fit residues: 47.6781 Evaluate side-chains 140 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 245 LEU 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 329 ILE 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 237 VAL 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: 0.6980 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 127 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 0.0070 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097106 restraints weight = 19612.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097757 restraints weight = 13291.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098847 restraints weight = 11120.014| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10916 Z= 0.182 Angle : 0.542 11.011 14740 Z= 0.271 Chirality : 0.041 0.184 1667 Planarity : 0.004 0.038 1905 Dihedral : 4.079 22.812 1477 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 14.65 % 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: 1.57 (0.24), residues: 1341 helix: 2.62 (0.21), residues: 642 sheet: -1.66 (0.91), residues: 20 loop : -0.44 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.014 0.001 PHE C 225 TYR 0.026 0.001 TYR B 51 ARG 0.004 0.000 ARG B 98 *********************** 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 151 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.247 Fit side-chains REVERT: C 181 MET cc_start: 0.9059 (mmm) cc_final: 0.8793 (tpt) REVERT: C 272 MET cc_start: 0.8729 (mtt) cc_final: 0.8321 (mtm) REVERT: D 195 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8350 (tt) REVERT: D 272 MET cc_start: 0.7589 (mmp) cc_final: 0.7165 (mmp) REVERT: E 151 LYS cc_start: 0.8061 (tmtm) cc_final: 0.7044 (mmtt) REVERT: E 199 ASP cc_start: 0.6178 (t0) cc_final: 0.5573 (p0) REVERT: F 196 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7570 (tp30) REVERT: F 260 GLU cc_start: 0.7532 (pm20) cc_final: 0.7288 (mp0) REVERT: F 338 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8815 (pp) outliers start: 32 outliers final: 25 residues processed: 143 average time/residue: 0.2198 time to fit residues: 46.3051 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 : 1.266 ------------------------------------------------------------------------------- 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 223 ASP Chi-restraints excluded: chain C residue 245 LEU 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 329 ILE 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 258 ASN Chi-restraints excluded: chain E residue 329 ILE 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: 3.9990 chunk 124 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.125783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098662 restraints weight = 19373.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099520 restraints weight = 13944.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099574 restraints weight = 12256.999| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10916 Z= 0.156 Angle : 0.549 10.784 14740 Z= 0.273 Chirality : 0.041 0.189 1667 Planarity : 0.003 0.039 1905 Dihedral : 4.032 21.944 1477 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.20 % Allowed : 15.33 % Favored : 82.47 % 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: 1.61 (0.24), residues: 1341 helix: 2.63 (0.21), residues: 642 sheet: -1.76 (0.90), residues: 20 loop : -0.39 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 146 HIS 0.004 0.001 HIS A 139 PHE 0.012 0.001 PHE C 225 TYR 0.025 0.001 TYR B 51 ARG 0.004 0.000 ARG B 98 ********************** 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 146 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.221 Fit side-chains REVERT: A 56 LYS cc_start: 0.7893 (tptm) cc_final: 0.7674 (tptm) REVERT: C 181 MET cc_start: 0.9026 (mmm) cc_final: 0.8760 (tpt) REVERT: C 272 MET cc_start: 0.8745 (mtt) cc_final: 0.8359 (mtm) REVERT: D 166 GLU cc_start: 0.7570 (tp30) cc_final: 0.7214 (tm-30) REVERT: D 195 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 272 MET cc_start: 0.7556 (mmp) cc_final: 0.7212 (mmp) REVERT: E 151 LYS cc_start: 0.8063 (tmtm) cc_final: 0.7052 (mmtt) REVERT: E 199 ASP cc_start: 0.6180 (t0) cc_final: 0.5600 (p0) REVERT: F 181 MET cc_start: 0.9008 (tpt) cc_final: 0.8805 (tpt) REVERT: F 196 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7600 (tp30) REVERT: F 338 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8838 (pp) outliers start: 26 outliers final: 22 residues processed: 139 average time/residue: 0.2197 time to fit residues: 44.2340 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 : 1.236 ------------------------------------------------------------------------------- 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 223 ASP Chi-restraints excluded: chain C residue 245 LEU 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 329 ILE 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 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: 0.0570 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096599 restraints weight = 19188.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097761 restraints weight = 13170.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098484 restraints weight = 11143.445| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10916 Z= 0.178 Angle : 0.551 10.381 14740 Z= 0.274 Chirality : 0.041 0.189 1667 Planarity : 0.004 0.038 1905 Dihedral : 4.044 22.184 1477 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.29 % Allowed : 15.07 % 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: 1.62 (0.24), residues: 1341 helix: 2.62 (0.21), residues: 642 sheet: -1.79 (0.93), residues: 20 loop : -0.37 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.007 0.001 HIS A 139 PHE 0.014 0.001 PHE C 225 TYR 0.023 0.001 TYR B 51 ARG 0.006 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.52 seconds wall clock time: 52 minutes 57.88 seconds (3177.88 seconds total)