Starting phenix.real_space_refine on Wed Jul 30 04:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.map" model { file = "/net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oit_20081/07_2025/6oit_20081.cif" } resolution = 3.5 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 71 5.16 5 C 7643 2.51 5 N 2101 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12085 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1010 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} 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: "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: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2619 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 325} 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: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1722 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2634 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2678 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 332} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 388 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.50, per 1000 atoms: 0.62 Number of scatterers: 12085 At special positions: 0 Unit cell: (98.44, 110.21, 145.52, 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 71 16.00 O 2270 8.00 N 2101 7.00 C 7643 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: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 54.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.589A pdb=" N SER A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 89 through 104 removed outlier: 4.078A pdb=" N ASP A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.667A pdb=" N GLU A 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 138 through 148 removed outlier: 4.214A pdb=" N MET A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.550A pdb=" N SER A 154 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 56 Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 89 through 102 removed outlier: 3.557A pdb=" N ASN B 93 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.597A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.921A pdb=" N THR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.996A pdb=" N SER B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 99 removed outlier: 4.123A pdb=" N SER C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.877A pdb=" N VAL C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.511A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.730A pdb=" N GLY C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 178 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.831A pdb=" N VAL C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 277 through 280 removed outlier: 3.761A 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: 3.630A pdb=" N ASN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.563A pdb=" N ALA C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.629A pdb=" N ILE C 318 " --> pdb=" O LEU C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 356 through 407 removed outlier: 3.935A pdb=" N TYR C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN C 394 " --> pdb=" O HIS C 390 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 removed outlier: 3.950A pdb=" N HIS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 139 removed outlier: 3.867A pdb=" N VAL D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) 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 165 through 177 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.881A pdb=" N VAL D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.857A pdb=" N ILE D 273 " --> pdb=" O VAL D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'E' and resid 47 through 98 removed outlier: 3.942A pdb=" N LEU E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.553A pdb=" N GLN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.858A pdb=" N VAL E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.814A pdb=" N LEU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.805A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.912A pdb=" N CYS E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 307 through 313 Processing helix chain 'E' and resid 314 through 318 removed outlier: 3.575A pdb=" N ILE E 318 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 405 removed outlier: 3.723A pdb=" N HIS E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 92 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.180A pdb=" N HIS F 125 " --> pdb=" O GLN F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.846A pdb=" N VAL F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.593A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 161 removed outlier: 4.032A pdb=" N GLY F 161 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 177 removed outlier: 3.668A pdb=" N GLY F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 3.552A pdb=" N VAL F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.548A pdb=" N LEU F 213 " --> pdb=" O GLY F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 273 removed outlier: 4.111A pdb=" N ILE F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 295 through 298 removed outlier: 3.531A pdb=" N LEU F 298 " --> pdb=" O PHE F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 358 through 408 Processing helix chain 'G' and resid 47 through 57 removed outlier: 3.587A pdb=" N ALA G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 186 removed outlier: 4.037A pdb=" N PHE C 225 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 227 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 336 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268 removed outlier: 3.940A pdb=" N GLY C 267 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 339 removed outlier: 6.656A pdb=" N VAL D 184 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.665A 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 removed outlier: 3.681A pdb=" N LYS D 162 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 267 through 268 removed outlier: 3.742A pdb=" N GLY D 267 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 removed outlier: 7.044A pdb=" N VAL E 185 " --> pdb=" O VAL E 154 " (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 225 through 228 Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.315A pdb=" N VAL E 304 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 338 through 339 removed outlier: 3.738A pdb=" N PHE F 225 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 184 through 186 removed outlier: 3.606A pdb=" N ILE F 228 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.148A pdb=" N VAL F 304 " --> pdb=" O LEU F 266 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1698 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: 3.07 Time building geometry restraints manager: 3.30 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: 2892 1.33 - 1.45: 2311 1.45 - 1.57: 6970 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12288 Sorted by residual: bond pdb=" N VAL F 283 " pdb=" CA VAL F 283 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE C 241 " pdb=" CA ILE C 241 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.26e+00 bond pdb=" N GLY F 289 " pdb=" CA GLY F 289 " ideal model delta sigma weight residual 1.445 1.473 -0.028 1.01e-02 9.80e+03 7.88e+00 bond pdb=" N VAL D 237 " pdb=" CA VAL D 237 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.52e+00 bond pdb=" N CYS F 282 " pdb=" CA CYS F 282 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.01e+00 ... (remaining 12283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 15800 2.12 - 4.23: 643 4.23 - 6.35: 77 6.35 - 8.47: 37 8.47 - 10.58: 13 Bond angle restraints: 16570 Sorted by residual: angle pdb=" C LEU F 252 " pdb=" N LYS F 253 " pdb=" CA LYS F 253 " ideal model delta sigma weight residual 120.94 130.86 -9.92 1.90e+00 2.77e-01 2.73e+01 angle pdb=" N THR A 136 " pdb=" CA THR A 136 " pdb=" C THR A 136 " ideal model delta sigma weight residual 109.81 120.39 -10.58 2.21e+00 2.05e-01 2.29e+01 angle pdb=" N THR B 136 " pdb=" CA THR B 136 " pdb=" C THR B 136 " ideal model delta sigma weight residual 109.81 119.89 -10.08 2.21e+00 2.05e-01 2.08e+01 angle pdb=" N GLU E 220 " pdb=" CA GLU E 220 " pdb=" C GLU E 220 " ideal model delta sigma weight residual 110.91 116.01 -5.10 1.17e+00 7.31e-01 1.90e+01 angle pdb=" CA GLY C 238 " pdb=" C GLY C 238 " pdb=" O GLY C 238 " ideal model delta sigma weight residual 121.47 117.63 3.84 9.00e-01 1.23e+00 1.82e+01 ... (remaining 16565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 6948 15.41 - 30.83: 399 30.83 - 46.24: 120 46.24 - 61.66: 13 61.66 - 77.07: 9 Dihedral angle restraints: 7489 sinusoidal: 3050 harmonic: 4439 Sorted by residual: dihedral pdb=" CA ILE D 318 " pdb=" C ILE D 318 " pdb=" N SER D 319 " pdb=" CA SER D 319 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PRO D 262 " pdb=" C PRO D 262 " pdb=" N PRO D 263 " pdb=" CA PRO D 263 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU E 256 " pdb=" C LEU E 256 " pdb=" N PRO E 257 " pdb=" CA PRO E 257 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1576 0.075 - 0.151: 249 0.151 - 0.226: 29 0.226 - 0.302: 10 0.302 - 0.377: 2 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CB ILE D 330 " pdb=" CA ILE D 330 " pdb=" CG1 ILE D 330 " pdb=" CG2 ILE D 330 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE F 228 " pdb=" CA ILE F 228 " pdb=" CG1 ILE F 228 " pdb=" CG2 ILE F 228 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU B 128 " pdb=" CB LEU B 128 " pdb=" CD1 LEU B 128 " pdb=" CD2 LEU B 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1863 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 234 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ARG D 234 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG D 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 235 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 234 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ARG F 234 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG F 234 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO F 235 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 386 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C VAL C 386 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL C 386 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU C 387 " -0.019 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1991 2.77 - 3.30: 11162 3.30 - 3.83: 18808 3.83 - 4.37: 21700 4.37 - 4.90: 37580 Nonbonded interactions: 91241 Sorted by model distance: nonbonded pdb=" O ILE F 273 " pdb=" NH2 ARG F 291 " model vdw 2.233 3.120 nonbonded pdb=" O GLN C 239 " pdb=" CB ASP C 250 " model vdw 2.247 3.440 nonbonded pdb=" O GLU E 166 " pdb=" OG SER E 169 " model vdw 2.308 3.040 nonbonded pdb=" O ILE A 132 " pdb=" OG1 THR A 136 " model vdw 2.321 3.040 nonbonded pdb=" O ARG E 301 " pdb=" OG SER E 319 " model vdw 2.327 3.040 ... (remaining 91236 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 161)) } ncs_group { reference = (chain 'C' and (resid 52 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 or resid 117 through 219 or ( \ resid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 \ through 352 or resid 357 through 405)) selection = (chain 'E' and (resid 52 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 or resid 117 through 352 or r \ esid 357 through 405)) selection = (chain 'F' and (resid 52 through 98 or resid 117 through 218 or (resid 219 throu \ gh 220 and (name N or name CA or name C or name O or name CB )) or resid 221 thr \ ough 405)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.006 0.066 12288 Z= 0.303 Angle : 1.020 10.583 16570 Z= 0.557 Chirality : 0.059 0.377 1866 Planarity : 0.008 0.071 2139 Dihedral : 11.442 77.069 4621 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.45 % Allowed : 7.18 % Favored : 92.37 % 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: -2.34 (0.18), residues: 1506 helix: -1.22 (0.16), residues: 732 sheet: -3.06 (0.83), residues: 30 loop : -1.78 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 127 HIS 0.018 0.003 HIS A 118 PHE 0.042 0.003 PHE A 104 TYR 0.022 0.002 TYR E 198 ARG 0.013 0.001 ARG F 308 Details of bonding type rmsd hydrogen bonds : bond 0.14935 ( 578) hydrogen bonds : angle 6.03550 ( 1698) covalent geometry : bond 0.00629 (12288) covalent geometry : angle 1.02020 (16570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 301 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8769 (tp30) cc_final: 0.8557 (tp30) REVERT: C 245 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8258 (mt) REVERT: C 357 MET cc_start: 0.7360 (ptp) cc_final: 0.7100 (ptm) REVERT: C 367 MET cc_start: 0.7778 (tpp) cc_final: 0.7271 (tpp) REVERT: G 74 MET cc_start: 0.7038 (tpt) cc_final: 0.6695 (tpp) outliers start: 6 outliers final: 2 residues processed: 307 average time/residue: 0.2781 time to fit residues: 118.0461 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain E residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 63 ASN B 118 HIS C 92 GLN C 174 ASN C 297 ASN D 201 HIS D 246 GLN D 297 ASN E 65 ASN E 232 ASN E 297 ASN E 303 GLN F 167 ASN F 297 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.186690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157210 restraints weight = 13947.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155661 restraints weight = 18441.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156313 restraints weight = 17540.154| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12288 Z= 0.139 Angle : 0.611 7.918 16570 Z= 0.314 Chirality : 0.042 0.170 1866 Planarity : 0.005 0.058 2139 Dihedral : 5.310 56.749 1656 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.87 % Allowed : 10.95 % Favored : 86.18 % 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: -0.58 (0.20), residues: 1506 helix: 0.66 (0.18), residues: 760 sheet: -2.78 (0.88), residues: 30 loop : -1.44 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 82 HIS 0.006 0.001 HIS A 118 PHE 0.022 0.002 PHE F 76 TYR 0.017 0.001 TYR D 286 ARG 0.007 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.05691 ( 578) hydrogen bonds : angle 4.25980 ( 1698) covalent geometry : bond 0.00310 (12288) covalent geometry : angle 0.61116 (16570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: B 64 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7935 (mtm-85) REVERT: C 245 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8136 (mt) REVERT: C 357 MET cc_start: 0.7393 (ptp) cc_final: 0.6919 (ptm) REVERT: E 63 MET cc_start: 0.7964 (mtt) cc_final: 0.7737 (mtm) REVERT: E 385 GLN cc_start: 0.7136 (mt0) cc_final: 0.6918 (mt0) REVERT: F 387 LEU cc_start: 0.8966 (tt) cc_final: 0.8726 (mp) outliers start: 38 outliers final: 15 residues processed: 214 average time/residue: 0.2456 time to fit residues: 75.7726 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 211 HIS D 246 GLN F 80 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.187482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156704 restraints weight = 14064.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154736 restraints weight = 22212.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156093 restraints weight = 18435.030| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12288 Z= 0.122 Angle : 0.548 7.471 16570 Z= 0.280 Chirality : 0.041 0.152 1866 Planarity : 0.004 0.053 2139 Dihedral : 4.790 53.124 1654 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.87 % Allowed : 12.16 % Favored : 84.97 % 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: 0.30 (0.21), residues: 1506 helix: 1.51 (0.19), residues: 763 sheet: -2.57 (0.89), residues: 30 loop : -1.17 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.006 0.001 HIS C 70 PHE 0.024 0.002 PHE F 76 TYR 0.013 0.001 TYR D 286 ARG 0.004 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 578) hydrogen bonds : angle 3.90336 ( 1698) covalent geometry : bond 0.00274 (12288) covalent geometry : angle 0.54844 (16570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: C 74 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 170 GLN cc_start: 0.7978 (tp40) cc_final: 0.7520 (tp40) REVERT: C 245 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (mt) REVERT: D 133 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5808 (tp) REVERT: E 63 MET cc_start: 0.7926 (mtt) cc_final: 0.7690 (mtm) REVERT: E 385 GLN cc_start: 0.7001 (mt0) cc_final: 0.6784 (mt0) REVERT: F 319 SER cc_start: 0.8172 (p) cc_final: 0.7961 (p) REVERT: F 367 MET cc_start: 0.8295 (tpp) cc_final: 0.7895 (tpp) REVERT: F 387 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8742 (mp) outliers start: 38 outliers final: 15 residues processed: 208 average time/residue: 0.2232 time to fit residues: 68.8084 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 140 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 overall best weight: 0.7566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 92 GLN D 246 GLN E 240 HIS E 345 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.187801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158101 restraints weight = 13877.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156435 restraints weight = 19322.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156610 restraints weight = 18926.482| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12288 Z= 0.118 Angle : 0.539 9.003 16570 Z= 0.268 Chirality : 0.041 0.182 1866 Planarity : 0.004 0.050 2139 Dihedral : 4.471 48.412 1654 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.02 % Allowed : 12.76 % Favored : 84.21 % 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: 0.84 (0.22), residues: 1506 helix: 2.06 (0.19), residues: 763 sheet: -2.43 (0.90), residues: 30 loop : -1.03 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.005 0.001 HIS B 141 PHE 0.023 0.001 PHE F 76 TYR 0.013 0.001 TYR C 296 ARG 0.004 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 578) hydrogen bonds : angle 3.69413 ( 1698) covalent geometry : bond 0.00266 (12288) covalent geometry : angle 0.53914 (16570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: C 74 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8189 (mt) REVERT: C 245 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 348 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7239 (t80) REVERT: D 133 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5725 (tp) REVERT: E 63 MET cc_start: 0.7941 (mtt) cc_final: 0.7694 (mtm) REVERT: E 385 GLN cc_start: 0.6939 (mt0) cc_final: 0.6727 (mt0) outliers start: 40 outliers final: 25 residues processed: 203 average time/residue: 0.2490 time to fit residues: 74.9736 Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 ASN D 246 GLN E 232 ASN E 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153013 restraints weight = 14064.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150767 restraints weight = 22636.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152727 restraints weight = 20639.132| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12288 Z= 0.170 Angle : 0.576 7.478 16570 Z= 0.291 Chirality : 0.043 0.225 1866 Planarity : 0.004 0.053 2139 Dihedral : 4.490 45.924 1653 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 13.90 % Favored : 83.16 % 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: 0.98 (0.22), residues: 1506 helix: 2.23 (0.19), residues: 756 sheet: -2.40 (0.90), residues: 30 loop : -1.00 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.006 0.001 HIS A 141 PHE 0.035 0.002 PHE F 76 TYR 0.015 0.001 TYR C 296 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 578) hydrogen bonds : angle 3.74128 ( 1698) covalent geometry : bond 0.00416 (12288) covalent geometry : angle 0.57555 (16570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: C 74 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (mt) REVERT: C 245 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8017 (mt) REVERT: C 348 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7386 (t80) REVERT: D 133 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5707 (tp) REVERT: E 63 MET cc_start: 0.7968 (mtt) cc_final: 0.7701 (mtm) REVERT: E 315 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8390 (mm) outliers start: 39 outliers final: 27 residues processed: 195 average time/residue: 0.2090 time to fit residues: 60.8660 Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN C 340 ASN D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156228 restraints weight = 14146.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155051 restraints weight = 19921.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155194 restraints weight = 17966.083| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12288 Z= 0.136 Angle : 0.554 9.776 16570 Z= 0.276 Chirality : 0.042 0.252 1866 Planarity : 0.004 0.048 2139 Dihedral : 4.331 41.419 1653 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.70 % Allowed : 14.20 % Favored : 82.10 % 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 (0.22), residues: 1506 helix: 2.39 (0.19), residues: 762 sheet: -2.36 (0.91), residues: 30 loop : -0.93 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.009 0.001 HIS B 141 PHE 0.036 0.002 PHE F 76 TYR 0.014 0.001 TYR C 296 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 578) hydrogen bonds : angle 3.60536 ( 1698) covalent geometry : bond 0.00327 (12288) covalent geometry : angle 0.55438 (16570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7582 (ttm170) REVERT: C 74 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8180 (mt) REVERT: C 245 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7980 (mt) REVERT: C 348 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7148 (t80) REVERT: D 133 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5800 (tp) REVERT: E 63 MET cc_start: 0.7933 (mtt) cc_final: 0.7723 (mtm) REVERT: F 178 THR cc_start: 0.8767 (t) cc_final: 0.8506 (m) REVERT: F 367 MET cc_start: 0.8029 (tpp) cc_final: 0.7815 (tpp) outliers start: 49 outliers final: 29 residues processed: 206 average time/residue: 0.2304 time to fit residues: 70.4867 Evaluate side-chains 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153766 restraints weight = 14139.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152801 restraints weight = 19829.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153704 restraints weight = 18039.869| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12288 Z= 0.157 Angle : 0.581 11.563 16570 Z= 0.287 Chirality : 0.043 0.323 1866 Planarity : 0.004 0.051 2139 Dihedral : 4.342 39.263 1653 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.32 % Allowed : 14.95 % Favored : 81.72 % 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: 1.24 (0.22), residues: 1506 helix: 2.45 (0.19), residues: 760 sheet: -2.39 (0.90), residues: 30 loop : -0.89 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.010 0.001 HIS B 141 PHE 0.036 0.002 PHE F 76 TYR 0.015 0.001 TYR C 296 ARG 0.003 0.000 ARG F 179 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 578) hydrogen bonds : angle 3.65140 ( 1698) covalent geometry : bond 0.00384 (12288) covalent geometry : angle 0.58109 (16570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: A 139 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6895 (m-70) REVERT: C 74 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8201 (mt) REVERT: C 245 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 348 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7068 (t80) REVERT: D 133 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5895 (tp) REVERT: E 63 MET cc_start: 0.7902 (mtt) cc_final: 0.7681 (mtm) REVERT: F 178 THR cc_start: 0.8774 (t) cc_final: 0.8507 (m) outliers start: 44 outliers final: 33 residues processed: 195 average time/residue: 0.2187 time to fit residues: 62.7936 Evaluate side-chains 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 118 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.187266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159397 restraints weight = 14174.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158523 restraints weight = 18708.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159729 restraints weight = 18056.500| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12288 Z= 0.109 Angle : 0.535 11.773 16570 Z= 0.264 Chirality : 0.040 0.300 1866 Planarity : 0.004 0.047 2139 Dihedral : 4.054 34.365 1653 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.95 % Allowed : 15.56 % Favored : 81.50 % 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: 1.52 (0.22), residues: 1506 helix: 2.68 (0.19), residues: 757 sheet: -2.29 (0.93), residues: 30 loop : -0.73 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 372 HIS 0.009 0.001 HIS B 141 PHE 0.011 0.001 PHE E 393 TYR 0.012 0.001 TYR C 296 ARG 0.002 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 578) hydrogen bonds : angle 3.47866 ( 1698) covalent geometry : bond 0.00250 (12288) covalent geometry : angle 0.53542 (16570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 139 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6899 (m-70) REVERT: C 74 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8172 (mt) REVERT: C 245 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8036 (mt) REVERT: C 348 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6812 (t80) REVERT: D 133 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5876 (tp) REVERT: D 272 MET cc_start: 0.6854 (mpt) cc_final: 0.6628 (mpt) REVERT: E 63 MET cc_start: 0.7910 (mtt) cc_final: 0.7695 (mtm) REVERT: F 178 THR cc_start: 0.8653 (t) cc_final: 0.8428 (m) outliers start: 39 outliers final: 26 residues processed: 195 average time/residue: 0.2193 time to fit residues: 62.9595 Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.186467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158320 restraints weight = 14022.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156933 restraints weight = 18431.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157112 restraints weight = 18377.416| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12288 Z= 0.137 Angle : 0.562 11.609 16570 Z= 0.278 Chirality : 0.042 0.312 1866 Planarity : 0.004 0.049 2139 Dihedral : 4.116 33.754 1653 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.87 % Allowed : 16.16 % Favored : 80.97 % 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: 1.48 (0.22), residues: 1506 helix: 2.63 (0.19), residues: 764 sheet: -2.17 (0.87), residues: 35 loop : -0.75 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.011 0.001 HIS B 141 PHE 0.038 0.002 PHE F 76 TYR 0.017 0.001 TYR C 175 ARG 0.007 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 578) hydrogen bonds : angle 3.50279 ( 1698) covalent geometry : bond 0.00330 (12288) covalent geometry : angle 0.56210 (16570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: A 139 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6978 (m-70) REVERT: C 74 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 245 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8052 (mt) REVERT: C 348 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6846 (t80) REVERT: D 133 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5899 (tp) REVERT: D 272 MET cc_start: 0.6916 (mpt) cc_final: 0.6656 (mpt) REVERT: E 63 MET cc_start: 0.7887 (mtt) cc_final: 0.7675 (mtm) REVERT: F 178 THR cc_start: 0.8708 (t) cc_final: 0.8485 (m) outliers start: 38 outliers final: 28 residues processed: 190 average time/residue: 0.2239 time to fit residues: 62.8370 Evaluate side-chains 189 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 0.0010 chunk 124 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.188246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163012 restraints weight = 13984.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161399 restraints weight = 22633.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.161635 restraints weight = 20288.475| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12288 Z= 0.112 Angle : 0.549 11.562 16570 Z= 0.270 Chirality : 0.041 0.311 1866 Planarity : 0.004 0.048 2139 Dihedral : 4.014 32.376 1653 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.64 % Allowed : 16.39 % Favored : 80.97 % 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: 1.64 (0.22), residues: 1506 helix: 2.75 (0.19), residues: 758 sheet: -2.20 (0.91), residues: 30 loop : -0.64 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.012 0.001 HIS B 141 PHE 0.017 0.001 PHE F 76 TYR 0.015 0.001 TYR C 175 ARG 0.002 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 578) hydrogen bonds : angle 3.46117 ( 1698) covalent geometry : bond 0.00256 (12288) covalent geometry : angle 0.54861 (16570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 139 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6989 (m-70) REVERT: C 74 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8257 (mt) REVERT: C 245 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8044 (mt) REVERT: C 348 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6729 (t80) REVERT: D 133 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5946 (tp) REVERT: D 272 MET cc_start: 0.6892 (mpt) cc_final: 0.6648 (mpt) REVERT: E 63 MET cc_start: 0.7856 (mtt) cc_final: 0.7649 (mtm) REVERT: F 178 THR cc_start: 0.8685 (t) cc_final: 0.8435 (m) outliers start: 35 outliers final: 26 residues processed: 185 average time/residue: 0.2214 time to fit residues: 59.7988 Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 115 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.186489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156293 restraints weight = 14008.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154106 restraints weight = 23642.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155441 restraints weight = 20018.462| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12288 Z= 0.147 Angle : 0.573 11.317 16570 Z= 0.283 Chirality : 0.043 0.310 1866 Planarity : 0.004 0.048 2139 Dihedral : 4.079 32.657 1653 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 16.24 % Favored : 80.97 % 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: 1.56 (0.22), residues: 1506 helix: 2.66 (0.19), residues: 763 sheet: -2.08 (0.88), residues: 35 loop : -0.66 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.012 0.001 HIS B 141 PHE 0.020 0.002 PHE F 395 TYR 0.022 0.001 TYR C 175 ARG 0.006 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 578) hydrogen bonds : angle 3.50274 ( 1698) covalent geometry : bond 0.00359 (12288) covalent geometry : angle 0.57295 (16570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.18 seconds wall clock time: 63 minutes 49.61 seconds (3829.61 seconds total)