Starting phenix.real_space_refine on Fri Jan 17 17:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fef_50340/01_2025/9fef_50340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fef_50340/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fef_50340/01_2025/9fef_50340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fef_50340/01_2025/9fef_50340.map" model { file = "/net/cci-nas-00/data/ceres_data/9fef_50340/01_2025/9fef_50340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fef_50340/01_2025/9fef_50340.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.46, per 1000 atoms: 0.67 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: 2.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.14 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: 3.48 Time building geometry restraints manager: 3.08 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: 1.670 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.680 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- 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= 0.727 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (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 TRP 0.008 0.001 TRP E 548 HIS 0.004 0.001 HIS C 268 PHE 0.011 0.001 PHE A 27 TYR 0.013 0.001 TYR E 568 ARG 0.004 0.000 ARG E 570 *********************** 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 : 1.132 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: 1.4578 time to fit residues: 169.3065 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 : 1.280 ------------------------------------------------------------------------------- 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 124 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109016 restraints weight = 11867.733| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.79 r_work: 0.3010 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11387 Z= 0.213 Angle : 0.592 11.152 15501 Z= 0.298 Chirality : 0.045 0.259 1875 Planarity : 0.005 0.074 2004 Dihedral : 5.098 50.658 1602 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.64 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1480 helix: 1.61 (0.19), residues: 779 sheet: -1.36 (0.38), residues: 158 loop : -1.46 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 PHE 0.012 0.001 PHE A 27 TYR 0.008 0.001 TYR C 194 ARG 0.003 0.000 ARG A 51 *********************** 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 153 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8008 (mttp) REVERT: B 235 MET cc_start: 0.8217 (tpt) cc_final: 0.7488 (mtp) REVERT: C 1 MET cc_start: 0.6352 (mtt) cc_final: 0.5716 (tmt) REVERT: C 228 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7346 (mtm110) outliers start: 44 outliers final: 15 residues processed: 140 average time/residue: 1.2790 time to fit residues: 194.7605 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106594 restraints weight = 11908.154| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.79 r_work: 0.2973 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11387 Z= 0.256 Angle : 0.602 8.462 15501 Z= 0.301 Chirality : 0.046 0.312 1875 Planarity : 0.005 0.094 2004 Dihedral : 4.962 52.467 1597 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.80 % Allowed : 21.84 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1480 helix: 1.59 (0.19), residues: 785 sheet: -1.36 (0.37), residues: 158 loop : -1.63 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 PHE 0.014 0.002 PHE A 27 TYR 0.008 0.001 TYR D 147 ARG 0.003 0.000 ARG C 171 *********************** 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 142 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8037 (mttp) REVERT: B 1 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6470 (pmm) REVERT: B 223 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7040 (tttp) REVERT: B 235 MET cc_start: 0.8250 (tpt) cc_final: 0.7552 (mtp) REVERT: C 1 MET cc_start: 0.6572 (mtt) cc_final: 0.5811 (tmt) REVERT: C 228 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7376 (mtm110) REVERT: C 275 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (pmm) REVERT: C 293 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7371 (pt) outliers start: 46 outliers final: 20 residues processed: 129 average time/residue: 1.4690 time to fit residues: 204.0351 Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 B residue 223 LYS 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 C residue 275 MET 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 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 E residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 439 ASN E 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108198 restraints weight = 11837.836| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.90 r_work: 0.3007 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11387 Z= 0.188 Angle : 0.559 7.258 15501 Z= 0.278 Chirality : 0.044 0.240 1875 Planarity : 0.005 0.098 2004 Dihedral : 4.784 50.016 1597 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.64 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1480 helix: 1.80 (0.19), residues: 784 sheet: -1.34 (0.38), residues: 158 loop : -1.57 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.003 0.001 HIS B 268 PHE 0.010 0.001 PHE B 27 TYR 0.019 0.001 TYR E 578 ARG 0.003 0.000 ARG E 570 *********************** 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 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6411 (pmm) REVERT: B 223 LYS cc_start: 0.7596 (ttmt) cc_final: 0.6958 (tttp) REVERT: B 235 MET cc_start: 0.8178 (tpt) cc_final: 0.7494 (mtp) REVERT: B 263 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (t0) REVERT: C 1 MET cc_start: 0.6595 (mtt) cc_final: 0.5845 (tmt) REVERT: C 275 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7978 (pmm) REVERT: D 303 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7265 (tp30) outliers start: 44 outliers final: 21 residues processed: 130 average time/residue: 1.3196 time to fit residues: 186.0712 Evaluate side-chains 119 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 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 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 275 MET 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 185 HIS Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 MET 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 83 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103582 restraints weight = 11902.431| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.87 r_work: 0.2932 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11387 Z= 0.320 Angle : 0.639 8.465 15501 Z= 0.318 Chirality : 0.047 0.207 1875 Planarity : 0.006 0.106 2004 Dihedral : 5.109 55.240 1597 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.96 % Allowed : 20.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1480 helix: 1.58 (0.19), residues: 785 sheet: -1.33 (0.37), residues: 158 loop : -1.72 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.007 0.001 HIS D 172 PHE 0.017 0.002 PHE A 27 TYR 0.011 0.001 TYR E 568 ARG 0.003 0.000 ARG A 51 *********************** 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 158 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 98 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7345 (tp30) REVERT: A 248 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8058 (mttp) REVERT: A 267 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: B 1 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6426 (pmm) REVERT: B 235 MET cc_start: 0.8274 (tpt) cc_final: 0.7557 (mtp) REVERT: C 1 MET cc_start: 0.6591 (mtt) cc_final: 0.5784 (tmt) REVERT: C 77 GLU cc_start: 0.8382 (tt0) cc_final: 0.8045 (tp30) REVERT: C 223 LYS cc_start: 0.7443 (ttpp) cc_final: 0.6617 (mptm) REVERT: C 293 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7429 (pt) REVERT: D 303 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: E 580 ARG cc_start: 0.1106 (OUTLIER) cc_final: 0.0873 (mmt180) outliers start: 60 outliers final: 25 residues processed: 139 average time/residue: 1.4116 time to fit residues: 211.8486 Evaluate side-chains 123 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 122 CYS 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 63 LEU 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 Chi-restraints excluded: chain D residue 185 HIS 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 146 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS B 268 HIS E 439 ASN E 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.155437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103719 restraints weight = 12029.172| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.90 r_work: 0.2934 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11387 Z= 0.296 Angle : 0.628 9.121 15501 Z= 0.311 Chirality : 0.046 0.224 1875 Planarity : 0.005 0.110 2004 Dihedral : 5.118 54.633 1597 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.38 % Allowed : 22.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1480 helix: 1.54 (0.19), residues: 786 sheet: -1.40 (0.37), residues: 158 loop : -1.76 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.006 0.001 HIS B 268 PHE 0.015 0.002 PHE A 27 TYR 0.012 0.001 TYR E 568 ARG 0.006 0.000 ARG A 51 *********************** 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 152 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: A 248 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (mttp) REVERT: B 223 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7011 (tttp) REVERT: B 235 MET cc_start: 0.8252 (tpt) cc_final: 0.7559 (mtp) REVERT: C 1 MET cc_start: 0.6589 (mtt) cc_final: 0.5746 (tmt) REVERT: C 77 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: C 286 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8033 (mtp180) REVERT: C 293 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7476 (pt) REVERT: D 303 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: E 555 LEU cc_start: 0.6397 (mt) cc_final: 0.6136 (mt) REVERT: E 568 TYR cc_start: 0.0320 (OUTLIER) cc_final: -0.0845 (t80) REVERT: E 580 ARG cc_start: 0.1118 (OUTLIER) cc_final: 0.0692 (mmt180) outliers start: 53 outliers final: 27 residues processed: 138 average time/residue: 1.2874 time to fit residues: 193.0268 Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 223 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 85 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 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 126 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 Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL 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 70 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.158967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107806 restraints weight = 12000.724| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.86 r_work: 0.2995 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11387 Z= 0.180 Angle : 0.580 10.889 15501 Z= 0.282 Chirality : 0.044 0.242 1875 Planarity : 0.005 0.112 2004 Dihedral : 4.828 51.126 1597 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.14 % Allowed : 22.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1480 helix: 1.83 (0.19), residues: 778 sheet: -1.27 (0.34), residues: 178 loop : -1.63 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.003 0.001 HIS D 172 PHE 0.017 0.001 PHE B 318 TYR 0.008 0.001 TYR E 568 ARG 0.004 0.000 ARG C 51 *********************** 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 139 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: B 17 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 223 LYS cc_start: 0.7592 (ttmt) cc_final: 0.6989 (tttp) REVERT: B 235 MET cc_start: 0.8192 (tpt) cc_final: 0.7510 (mtp) REVERT: C 1 MET cc_start: 0.6489 (mtt) cc_final: 0.5695 (tmt) REVERT: C 223 LYS cc_start: 0.7379 (ttpp) cc_final: 0.6533 (mptm) REVERT: C 286 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8024 (mtp180) REVERT: C 293 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7296 (pt) REVERT: D 303 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: E 555 LEU cc_start: 0.6429 (mt) cc_final: 0.6171 (mt) REVERT: E 568 TYR cc_start: 0.0320 (OUTLIER) cc_final: -0.0621 (t80) outliers start: 38 outliers final: 24 residues processed: 128 average time/residue: 1.2635 time to fit residues: 175.7902 Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 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 17 LEU 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 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 17 LEU 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 136 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL 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 2 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.158061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106270 restraints weight = 11939.256| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.80 r_work: 0.2975 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1786 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= 0.209 Angle : 0.602 15.655 15501 Z= 0.291 Chirality : 0.044 0.184 1875 Planarity : 0.005 0.116 2004 Dihedral : 4.866 51.688 1597 Min Nonbonded Distance : 2.551 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1480 helix: 1.82 (0.19), residues: 780 sheet: -1.24 (0.34), residues: 178 loop : -1.61 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 PHE 0.012 0.001 PHE B 318 TYR 0.008 0.001 TYR E 568 ARG 0.003 0.000 ARG A 51 *********************** 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 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: B 223 LYS cc_start: 0.7584 (ttmt) cc_final: 0.6965 (tttp) REVERT: B 235 MET cc_start: 0.8234 (tpt) cc_final: 0.7523 (mtp) REVERT: B 263 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8558 (t0) REVERT: C 1 MET cc_start: 0.6477 (mtt) cc_final: 0.5693 (tmt) REVERT: C 286 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8021 (mtp180) REVERT: C 293 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7328 (pt) REVERT: D 303 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: E 555 LEU cc_start: 0.6373 (mt) cc_final: 0.6119 (mt) REVERT: E 568 TYR cc_start: 0.0447 (OUTLIER) cc_final: -0.0610 (t80) REVERT: E 580 ARG cc_start: 0.1139 (OUTLIER) cc_final: 0.0616 (mmt180) outliers start: 44 outliers final: 25 residues processed: 132 average time/residue: 1.2640 time to fit residues: 180.8513 Evaluate side-chains 130 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 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 136 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 568 TYR Chi-restraints excluded: chain E residue 580 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106673 restraints weight = 12003.701| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.89 r_work: 0.2979 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1824 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= 0.201 Angle : 0.605 14.627 15501 Z= 0.292 Chirality : 0.044 0.193 1875 Planarity : 0.005 0.118 2004 Dihedral : 4.841 51.069 1597 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1480 helix: 1.87 (0.19), residues: 780 sheet: -1.22 (0.34), residues: 178 loop : -1.58 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 PHE 0.012 0.001 PHE B 318 TYR 0.008 0.001 TYR E 568 ARG 0.003 0.000 ARG A 51 *********************** 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 135 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: B 223 LYS cc_start: 0.7533 (ttmt) cc_final: 0.6910 (tttp) REVERT: B 235 MET cc_start: 0.8193 (tpt) cc_final: 0.7475 (mtp) REVERT: B 263 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (t0) REVERT: C 1 MET cc_start: 0.6523 (mtt) cc_final: 0.5693 (tmt) REVERT: C 286 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: C 293 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7254 (pt) REVERT: D 303 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: E 555 LEU cc_start: 0.6317 (mt) cc_final: 0.6061 (mt) REVERT: E 568 TYR cc_start: 0.0395 (OUTLIER) cc_final: -0.0766 (t80) outliers start: 38 outliers final: 26 residues processed: 124 average time/residue: 1.3217 time to fit residues: 177.3174 Evaluate side-chains 131 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 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 63 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL 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 77 optimal weight: 0.0020 chunk 113 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 C 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 = 0.3767 r_free = 0.3767 target = 0.160965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109268 restraints weight = 11915.808| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.80 r_work: 0.3032 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11387 Z= 0.165 Angle : 0.588 14.322 15501 Z= 0.280 Chirality : 0.043 0.196 1875 Planarity : 0.005 0.120 2004 Dihedral : 4.650 48.674 1597 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.56 % Allowed : 23.57 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1480 helix: 2.03 (0.19), residues: 778 sheet: -1.17 (0.35), residues: 178 loop : -1.47 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.003 0.001 HIS B 58 PHE 0.015 0.001 PHE B 318 TYR 0.007 0.001 TYR B 261 ARG 0.002 0.000 ARG A 51 ********************** 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 130 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.7757 (tpt) cc_final: 0.7382 (mmt) REVERT: A 237 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: B 223 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6857 (tttp) REVERT: B 235 MET cc_start: 0.8122 (tpt) cc_final: 0.7420 (mtp) REVERT: B 263 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8488 (t0) REVERT: C 1 MET cc_start: 0.6471 (mtt) cc_final: 0.5701 (tmt) REVERT: C 286 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7969 (mtp180) REVERT: D 1 MET cc_start: 0.6526 (ptp) cc_final: 0.5217 (ttm) REVERT: E 555 LEU cc_start: 0.6219 (mt) cc_final: 0.5953 (mt) REVERT: E 568 TYR cc_start: 0.0647 (OUTLIER) cc_final: -0.0562 (t80) outliers start: 31 outliers final: 20 residues processed: 121 average time/residue: 1.3235 time to fit residues: 173.4228 Evaluate side-chains 124 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL 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 E residue 568 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 133 optimal weight: 50.0000 chunk 91 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105814 restraints weight = 11726.079| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.89 r_work: 0.2972 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1937 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= 0.225 Angle : 0.632 14.396 15501 Z= 0.300 Chirality : 0.045 0.195 1875 Planarity : 0.005 0.116 2004 Dihedral : 4.781 47.713 1597 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.56 % Allowed : 23.57 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1480 helix: 1.88 (0.19), residues: 780 sheet: -1.16 (0.35), residues: 178 loop : -1.55 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 PHE 0.012 0.002 PHE A 27 TYR 0.010 0.001 TYR E 568 ARG 0.002 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7198.38 seconds wall clock time: 129 minutes 36.50 seconds (7776.50 seconds total)