Starting phenix.real_space_refine on Sat Aug 23 09:11:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fef_50340/08_2025/9fef_50340.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7106 2.51 5 N 1959 2.21 5 O 2065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11192 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2320 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 291} Chain breaks: 1 Chain: "B" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2304 Classifications: {'peptide': 312} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 289} Chain breaks: 1 Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2326 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2320 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 22, 'TRANS': 291} Chain breaks: 1 Chain: "E" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1922 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 2 Time building chain proxies: 2.76, per 1000 atoms: 0.25 Number of scatterers: 11192 At special positions: 0 Unit cell: (88.2, 102.48, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2065 8.00 N 1959 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 565.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 55.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 4.041A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.510A pdb=" N ASP A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.193A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.524A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.607A pdb=" N GLU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.684A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.969A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.675A pdb=" N VAL B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.688A pdb=" N SER B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.651A pdb=" N THR B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix removed outlier: 3.602A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.227A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.916A pdb=" N ILE B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.882A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.807A pdb=" N MET B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 318 removed outlier: 3.919A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 4.202A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.767A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 97 through 116 removed outlier: 3.871A pdb=" N ASN C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 157 through 171 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.867A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 294 through 320 removed outlier: 3.822A pdb=" N GLU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 3.817A pdb=" N GLN D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 4.453A pdb=" N ASP D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 removed outlier: 3.513A pdb=" N GLU D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.364A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.250A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.755A pdb=" N ILE D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.523A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 251 removed outlier: 3.578A pdb=" N MET D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 319 removed outlier: 3.734A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.726A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 382 Processing helix chain 'E' and resid 395 through 404 Processing helix chain 'E' and resid 408 through 423 Processing helix chain 'E' and resid 426 through 440 removed outlier: 3.652A pdb=" N HIS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 457 removed outlier: 3.815A pdb=" N GLN E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 507 Processing helix chain 'E' and resid 510 through 523 removed outlier: 3.515A pdb=" N LEU E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 Processing helix chain 'E' and resid 544 through 558 removed outlier: 3.602A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.791A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 611 removed outlier: 3.518A pdb=" N ALA E 598 " --> pdb=" O GLN E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 638 removed outlier: 3.893A pdb=" N GLY E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 627 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 637 " --> pdb=" O MET E 633 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 638 " --> pdb=" O THR E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 648 removed outlier: 3.680A pdb=" N TRP E 648 " --> pdb=" O VAL E 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.290A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.699A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.081A pdb=" N LEU B 31 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA B 59 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 3 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL B 83 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 5 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 261 removed outlier: 3.614A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.084A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN C 3 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 83 " --> pdb=" O ASN C 3 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 5 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 82 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 261 removed outlier: 3.764A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.961A pdb=" N ASP D 35 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 6 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 259 removed outlier: 5.160A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.09: 1 1.09 - 1.31: 1881 1.31 - 1.53: 7788 1.53 - 1.75: 1611 1.75 - 1.97: 106 Bond restraints: 11387 Sorted by residual: bond pdb=" CG PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 1.503 0.865 0.638 3.40e-02 8.65e+02 3.53e+02 bond pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 1.492 1.968 -0.476 5.00e-02 4.00e+02 9.05e+01 bond pdb=" N PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta sigma weight residual 1.534 1.441 0.093 1.79e-02 3.12e+03 2.70e+01 bond pdb=" C HIS D 172 " pdb=" N PRO D 173 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.06e-02 8.90e+03 1.65e+01 ... (remaining 11382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 15484 6.64 - 13.27: 12 13.27 - 19.91: 2 19.91 - 26.55: 0 26.55 - 33.19: 3 Bond angle restraints: 15501 Sorted by residual: angle pdb=" N PRO D 173 " pdb=" CD PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 103.20 70.01 33.19 1.50e+00 4.44e-01 4.90e+02 angle pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 104.50 72.67 31.83 1.90e+00 2.77e-01 2.81e+02 angle pdb=" N PRO D 173 " pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta sigma weight residual 103.20 88.39 14.81 9.50e-01 1.11e+00 2.43e+02 angle pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 106.10 74.71 31.39 3.20e+00 9.77e-02 9.62e+01 angle pdb=" CA PRO D 173 " pdb=" N PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.69e+01 ... (remaining 15496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5980 17.93 - 35.87: 723 35.87 - 53.80: 189 53.80 - 71.74: 32 71.74 - 89.67: 11 Dihedral angle restraints: 6935 sinusoidal: 2666 harmonic: 4269 Sorted by residual: dihedral pdb=" CA HIS D 172 " pdb=" C HIS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta harmonic sigma weight residual 180.00 126.91 53.09 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA E 564 " pdb=" C ALA E 564 " pdb=" N LEU E 565 " pdb=" CA LEU E 565 " ideal model delta harmonic sigma weight residual 180.00 135.67 44.33 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" N PRO D 173 " pdb=" C PRO D 173 " pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta harmonic sigma weight residual 115.10 96.71 18.39 0 2.50e+00 1.60e-01 5.41e+01 ... (remaining 6932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1651 0.071 - 0.142: 218 0.142 - 0.213: 3 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1875 Sorted by residual: chirality pdb=" CA ASN C 128 " pdb=" N ASN C 128 " pdb=" C ASN C 128 " pdb=" CB ASN C 128 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1872 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 172 " -0.101 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO D 173 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 127 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR C 127 " -0.075 2.00e-02 2.50e+03 pdb=" O THR C 127 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN C 128 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 128 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASN C 128 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN C 128 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO C 129 " -0.021 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 10977 3.26 - 3.81: 17850 3.81 - 4.35: 21756 4.35 - 4.90: 37846 Nonbonded interactions: 88812 Sorted by model distance: nonbonded pdb=" O LEU C 25 " pdb=" NH2 ARG C 51 " model vdw 2.173 3.120 nonbonded pdb=" O LEU A 25 " pdb=" NH2 ARG A 51 " model vdw 2.206 3.120 nonbonded pdb=" OG1 THR A 264 " pdb=" O CYS A 270 " model vdw 2.216 3.040 nonbonded pdb=" O LEU B 25 " pdb=" NH2 ARG B 51 " model vdw 2.247 3.120 nonbonded pdb=" O ASN C 128 " pdb=" N VAL C 130 " model vdw 2.288 3.120 ... (remaining 88807 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' and resid 1 through 318) selection = chain 'B' selection = (chain 'C' and resid 1 through 318) selection = (chain 'D' and resid 1 through 318) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.950 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.008 0.638 11387 Z= 0.281 Angle : 0.830 33.187 15501 Z= 0.479 Chirality : 0.046 0.355 1875 Planarity : 0.006 0.146 2004 Dihedral : 16.727 89.670 4187 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 0.58 % Allowed : 23.74 % Favored : 75.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.22), residues: 1480 helix: 1.47 (0.19), residues: 764 sheet: -1.44 (0.38), residues: 158 loop : -1.49 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 570 TYR 0.013 0.001 TYR E 568 PHE 0.011 0.001 PHE A 27 TRP 0.008 0.001 TRP E 548 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00827 (11387) covalent geometry : angle 0.83017 (15501) hydrogen bonds : bond 0.15242 ( 560) hydrogen bonds : angle 4.99414 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 0.6890 time to fit residues: 79.4761 Evaluate side-chains 96 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 132 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 172 HIS ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106624 restraints weight = 11957.732| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.79 r_work: 0.2964 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11387 Z= 0.182 Angle : 0.645 12.561 15501 Z= 0.326 Chirality : 0.047 0.299 1875 Planarity : 0.006 0.077 2004 Dihedral : 5.292 52.992 1602 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.89 % Allowed : 22.00 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1480 helix: 1.42 (0.19), residues: 781 sheet: -1.43 (0.37), residues: 158 loop : -1.66 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 171 TYR 0.011 0.001 TYR C 194 PHE 0.016 0.002 PHE A 27 TRP 0.008 0.001 TRP E 548 HIS 0.008 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00451 (11387) covalent geometry : angle 0.64501 (15501) hydrogen bonds : bond 0.04638 ( 560) hydrogen bonds : angle 3.85637 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: B 235 MET cc_start: 0.8225 (tpt) cc_final: 0.7498 (mtp) REVERT: C 1 MET cc_start: 0.6439 (mtt) cc_final: 0.5775 (tmt) REVERT: C 228 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7314 (mtm110) REVERT: D 81 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7792 (t) outliers start: 47 outliers final: 17 residues processed: 135 average time/residue: 0.5870 time to fit residues: 85.7645 Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 0.0010 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 559 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110036 restraints weight = 11896.505| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.81 r_work: 0.3016 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11387 Z= 0.114 Angle : 0.556 7.650 15501 Z= 0.278 Chirality : 0.044 0.321 1875 Planarity : 0.005 0.087 2004 Dihedral : 4.814 50.339 1597 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.39 % Allowed : 22.50 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1480 helix: 1.71 (0.19), residues: 780 sheet: -1.39 (0.37), residues: 158 loop : -1.55 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.007 0.001 TYR B 261 PHE 0.014 0.001 PHE B 318 TRP 0.007 0.001 TRP E 548 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00263 (11387) covalent geometry : angle 0.55629 (15501) hydrogen bonds : bond 0.03262 ( 560) hydrogen bonds : angle 3.51702 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6408 (pmm) REVERT: B 223 LYS cc_start: 0.7644 (ttmt) cc_final: 0.6997 (tttp) REVERT: B 235 MET cc_start: 0.8177 (tpt) cc_final: 0.7503 (mtp) REVERT: C 1 MET cc_start: 0.6628 (mtt) cc_final: 0.5868 (tmt) REVERT: C 293 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7269 (pt) REVERT: D 47 SER cc_start: 0.8781 (p) cc_final: 0.8514 (m) REVERT: D 303 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: E 555 LEU cc_start: 0.6669 (mt) cc_final: 0.6434 (mt) outliers start: 41 outliers final: 20 residues processed: 138 average time/residue: 0.5649 time to fit residues: 84.2065 Evaluate side-chains 121 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN B 172 HIS E 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108666 restraints weight = 11987.038| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.84 r_work: 0.3015 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11387 Z= 0.117 Angle : 0.558 7.661 15501 Z= 0.278 Chirality : 0.044 0.242 1875 Planarity : 0.005 0.097 2004 Dihedral : 4.736 49.693 1597 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.80 % Allowed : 22.00 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1480 helix: 1.79 (0.19), residues: 787 sheet: -1.31 (0.38), residues: 158 loop : -1.55 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 570 TYR 0.019 0.001 TYR E 578 PHE 0.011 0.001 PHE B 27 TRP 0.005 0.001 TRP E 548 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00273 (11387) covalent geometry : angle 0.55784 (15501) hydrogen bonds : bond 0.03291 ( 560) hydrogen bonds : angle 3.44364 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: B 1 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6388 (pmm) REVERT: B 223 LYS cc_start: 0.7624 (ttmt) cc_final: 0.6982 (tttp) REVERT: B 235 MET cc_start: 0.8168 (tpt) cc_final: 0.7483 (mtp) REVERT: B 263 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8487 (t0) REVERT: C 1 MET cc_start: 0.6608 (mtt) cc_final: 0.5856 (tmt) REVERT: C 244 MET cc_start: 0.8564 (mmm) cc_final: 0.8342 (mmp) REVERT: C 293 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7211 (pt) REVERT: D 47 SER cc_start: 0.8772 (p) cc_final: 0.8468 (m) REVERT: D 303 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7261 (tp30) outliers start: 46 outliers final: 21 residues processed: 132 average time/residue: 0.5452 time to fit residues: 78.1149 Evaluate side-chains 125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 439 ASN E 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108136 restraints weight = 11868.162| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.88 r_work: 0.2998 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11387 Z= 0.123 Angle : 0.567 7.882 15501 Z= 0.281 Chirality : 0.044 0.233 1875 Planarity : 0.005 0.101 2004 Dihedral : 4.758 50.527 1597 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.22 % Allowed : 21.84 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1480 helix: 1.84 (0.19), residues: 786 sheet: -1.27 (0.38), residues: 158 loop : -1.54 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.010 0.001 TYR E 568 PHE 0.011 0.001 PHE A 27 TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00293 (11387) covalent geometry : angle 0.56705 (15501) hydrogen bonds : bond 0.03352 ( 560) hydrogen bonds : angle 3.41719 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: A 267 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: B 1 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6483 (pmm) REVERT: B 223 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7022 (tttp) REVERT: B 235 MET cc_start: 0.8223 (tpt) cc_final: 0.7535 (mtp) REVERT: C 1 MET cc_start: 0.6596 (mtt) cc_final: 0.5857 (tmt) REVERT: C 223 LYS cc_start: 0.7414 (ttpp) cc_final: 0.6580 (mptm) REVERT: C 286 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8048 (mtp180) REVERT: C 293 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7261 (pt) REVERT: D 303 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: E 580 ARG cc_start: 0.1102 (OUTLIER) cc_final: 0.0710 (mmt180) outliers start: 51 outliers final: 25 residues processed: 133 average time/residue: 0.5611 time to fit residues: 80.4793 Evaluate side-chains 128 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 580 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS D 131 ASN E 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107502 restraints weight = 11934.474| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.85 r_work: 0.2990 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11387 Z= 0.120 Angle : 0.571 9.239 15501 Z= 0.280 Chirality : 0.044 0.239 1875 Planarity : 0.005 0.107 2004 Dihedral : 4.724 50.127 1597 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.05 % Allowed : 22.17 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.22), residues: 1480 helix: 1.94 (0.19), residues: 780 sheet: -1.18 (0.35), residues: 178 loop : -1.54 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 51 TYR 0.008 0.001 TYR E 568 PHE 0.011 0.001 PHE A 27 TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00287 (11387) covalent geometry : angle 0.57055 (15501) hydrogen bonds : bond 0.03269 ( 560) hydrogen bonds : angle 3.36516 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: B 1 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6379 (pmm) REVERT: B 223 LYS cc_start: 0.7611 (ttmt) cc_final: 0.6987 (tttp) REVERT: B 235 MET cc_start: 0.8227 (tpt) cc_final: 0.7519 (mtp) REVERT: B 263 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8525 (t0) REVERT: C 1 MET cc_start: 0.6547 (mtt) cc_final: 0.5767 (tmt) REVERT: C 223 LYS cc_start: 0.7352 (ttpp) cc_final: 0.6514 (mptm) REVERT: C 286 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: C 293 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7236 (pt) REVERT: D 303 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: E 555 LEU cc_start: 0.6398 (mt) cc_final: 0.6146 (mt) REVERT: E 568 TYR cc_start: 0.0193 (OUTLIER) cc_final: -0.0900 (t80) REVERT: E 580 ARG cc_start: 0.1146 (OUTLIER) cc_final: 0.0597 (mmt180) outliers start: 49 outliers final: 26 residues processed: 131 average time/residue: 0.5314 time to fit residues: 75.1292 Evaluate side-chains 128 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 568 TYR Chi-restraints excluded: chain E residue 580 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 0.0000 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 172 HIS D 131 ASN E 514 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110425 restraints weight = 11933.676| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.80 r_work: 0.3041 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11387 Z= 0.100 Angle : 0.542 8.964 15501 Z= 0.266 Chirality : 0.043 0.208 1875 Planarity : 0.005 0.109 2004 Dihedral : 4.558 48.288 1597 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.64 % Allowed : 22.42 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1480 helix: 2.12 (0.19), residues: 778 sheet: -1.15 (0.35), residues: 178 loop : -1.42 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 51 TYR 0.007 0.001 TYR B 261 PHE 0.009 0.001 PHE B 318 TRP 0.005 0.001 TRP E 548 HIS 0.002 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00227 (11387) covalent geometry : angle 0.54155 (15501) hydrogen bonds : bond 0.02768 ( 560) hydrogen bonds : angle 3.25406 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: B 223 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6934 (tttp) REVERT: B 235 MET cc_start: 0.8151 (tpt) cc_final: 0.7432 (mtp) REVERT: B 263 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8509 (t0) REVERT: C 1 MET cc_start: 0.6561 (mtt) cc_final: 0.5795 (tmt) REVERT: C 223 LYS cc_start: 0.7361 (ttpp) cc_final: 0.6509 (mptm) REVERT: C 286 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8024 (mtp180) REVERT: C 293 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7128 (pt) REVERT: D 47 SER cc_start: 0.8724 (p) cc_final: 0.8469 (m) REVERT: D 303 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: E 555 LEU cc_start: 0.6485 (mt) cc_final: 0.6224 (mt) REVERT: E 568 TYR cc_start: 0.0250 (OUTLIER) cc_final: -0.0703 (t80) outliers start: 44 outliers final: 26 residues processed: 129 average time/residue: 0.4450 time to fit residues: 62.2955 Evaluate side-chains 135 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 568 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107144 restraints weight = 11910.519| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.83 r_work: 0.2992 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11387 Z= 0.135 Angle : 0.590 9.606 15501 Z= 0.288 Chirality : 0.044 0.193 1875 Planarity : 0.005 0.102 2004 Dihedral : 4.689 47.135 1597 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.64 % Allowed : 22.42 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.22), residues: 1480 helix: 1.97 (0.19), residues: 780 sheet: -1.18 (0.35), residues: 178 loop : -1.52 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.008 0.001 TYR E 568 PHE 0.012 0.001 PHE A 27 TRP 0.005 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00331 (11387) covalent geometry : angle 0.59049 (15501) hydrogen bonds : bond 0.03489 ( 560) hydrogen bonds : angle 3.34828 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: B 223 LYS cc_start: 0.7604 (ttmt) cc_final: 0.6990 (tttm) REVERT: B 235 MET cc_start: 0.8207 (tpt) cc_final: 0.7526 (mtp) REVERT: B 263 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8547 (t0) REVERT: C 1 MET cc_start: 0.6532 (mtt) cc_final: 0.5759 (tmt) REVERT: C 157 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8490 (tt) REVERT: C 286 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: C 293 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7246 (pt) REVERT: D 1 MET cc_start: 0.6685 (ptp) cc_final: 0.5234 (ttm) REVERT: D 303 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: E 555 LEU cc_start: 0.6390 (mt) cc_final: 0.6137 (mt) REVERT: E 568 TYR cc_start: 0.0400 (OUTLIER) cc_final: -0.0560 (t80) outliers start: 44 outliers final: 27 residues processed: 133 average time/residue: 0.4825 time to fit residues: 69.3652 Evaluate side-chains 134 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 chunk 137 optimal weight: 0.0670 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106550 restraints weight = 11804.367| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.86 r_work: 0.2976 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11387 Z= 0.127 Angle : 0.579 11.014 15501 Z= 0.284 Chirality : 0.044 0.187 1875 Planarity : 0.005 0.096 2004 Dihedral : 4.687 45.721 1597 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.98 % Allowed : 22.91 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.22), residues: 1480 helix: 1.97 (0.19), residues: 780 sheet: -1.16 (0.35), residues: 178 loop : -1.54 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.008 0.001 TYR E 568 PHE 0.012 0.001 PHE A 27 TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00308 (11387) covalent geometry : angle 0.57936 (15501) hydrogen bonds : bond 0.03361 ( 560) hydrogen bonds : angle 3.31146 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: B 223 LYS cc_start: 0.7529 (ttmt) cc_final: 0.6890 (tttm) REVERT: B 235 MET cc_start: 0.8170 (tpt) cc_final: 0.7421 (mtp) REVERT: B 263 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8531 (t0) REVERT: C 1 MET cc_start: 0.6507 (mtt) cc_final: 0.5676 (tmt) REVERT: C 157 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8462 (tt) REVERT: C 244 MET cc_start: 0.8558 (mmm) cc_final: 0.8348 (mmp) REVERT: C 286 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7939 (mtp180) REVERT: C 293 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7157 (pt) REVERT: D 1 MET cc_start: 0.6710 (ptp) cc_final: 0.5228 (ttm) REVERT: D 303 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: E 555 LEU cc_start: 0.6412 (mt) cc_final: 0.6158 (mt) REVERT: E 568 TYR cc_start: 0.0651 (OUTLIER) cc_final: -0.0538 (t80) outliers start: 36 outliers final: 25 residues processed: 121 average time/residue: 0.4864 time to fit residues: 63.5967 Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106235 restraints weight = 11907.714| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.88 r_work: 0.2977 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11387 Z= 0.140 Angle : 0.604 10.002 15501 Z= 0.294 Chirality : 0.045 0.184 1875 Planarity : 0.005 0.097 2004 Dihedral : 4.755 46.602 1597 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.14 % Allowed : 22.83 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.22), residues: 1480 helix: 1.90 (0.19), residues: 780 sheet: -1.17 (0.34), residues: 178 loop : -1.56 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.010 0.001 TYR E 568 PHE 0.012 0.002 PHE A 27 TRP 0.005 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00342 (11387) covalent geometry : angle 0.60369 (15501) hydrogen bonds : bond 0.03596 ( 560) hydrogen bonds : angle 3.35133 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: B 223 LYS cc_start: 0.7561 (ttmt) cc_final: 0.6926 (tttm) REVERT: B 235 MET cc_start: 0.8175 (tpt) cc_final: 0.7453 (mtp) REVERT: B 263 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (t0) REVERT: C 1 MET cc_start: 0.6483 (mtt) cc_final: 0.5689 (tmt) REVERT: C 157 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8478 (tt) REVERT: C 286 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7948 (mtp180) REVERT: C 293 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7235 (pt) REVERT: D 1 MET cc_start: 0.6694 (ptp) cc_final: 0.5255 (ttm) REVERT: D 303 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: E 555 LEU cc_start: 0.6347 (mt) cc_final: 0.6090 (mt) REVERT: E 568 TYR cc_start: 0.0461 (OUTLIER) cc_final: -0.0520 (t80) outliers start: 38 outliers final: 27 residues processed: 128 average time/residue: 0.5558 time to fit residues: 76.8683 Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 125 optimal weight: 0.0270 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108471 restraints weight = 11929.570| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.85 r_work: 0.3008 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11387 Z= 0.105 Angle : 0.569 9.821 15501 Z= 0.275 Chirality : 0.043 0.179 1875 Planarity : 0.005 0.092 2004 Dihedral : 4.555 44.032 1597 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.14 % Allowed : 23.24 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.22), residues: 1480 helix: 2.07 (0.19), residues: 780 sheet: -1.13 (0.35), residues: 178 loop : -1.45 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.009 0.001 TYR E 568 PHE 0.008 0.001 PHE A 27 TRP 0.004 0.001 TRP E 548 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00245 (11387) covalent geometry : angle 0.56893 (15501) hydrogen bonds : bond 0.02889 ( 560) hydrogen bonds : angle 3.25349 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3465.54 seconds wall clock time: 59 minutes 54.60 seconds (3594.60 seconds total)