Starting phenix.real_space_refine on Mon Aug 25 15:49:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.map" model { file = "/net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8c_25744/08_2025/7t8c_25744.cif" } resolution = 4.5 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= 0.001 sd= 0.024 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 105 5.16 5 C 18480 2.51 5 N 5075 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s 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: 28952 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4136 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.35, per 1000 atoms: 0.12 Number of scatterers: 28952 At special positions: 0 Unit cell: (187.266, 188.324, 83.582, 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 105 16.00 O 5292 8.00 N 5075 7.00 C 18480 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: 2.06 Conformation dependent library (CDL) restraints added in 867.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 28 sheets defined 44.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 56 through 68 removed outlier: 3.606A pdb=" N HIS A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 181 Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.528A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 291 through 299 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA A 388 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 68 removed outlier: 3.606A pdb=" N HIS B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 186 through 194 removed outlier: 3.528A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 266 through 276 Processing helix chain 'B' and resid 291 through 299 Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.095A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 550 Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS C 67 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 291 through 299 Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA C 388 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE C 401 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 550 Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 186 through 194 removed outlier: 3.527A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 291 through 299 Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE D 424 " --> pdb=" O GLY D 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 425 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 461 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 493 through 509 Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 550 Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS E 67 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 181 Processing helix chain 'E' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 266 through 276 Processing helix chain 'E' and resid 291 through 299 Proline residue: E 296 - end of helix Processing helix chain 'E' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 358 Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.095A pdb=" N ALA E 388 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE E 424 " --> pdb=" O GLY E 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 426 " --> pdb=" O THR E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 461 Processing helix chain 'E' and resid 471 through 479 Processing helix chain 'E' and resid 493 through 509 Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY E 523 " --> pdb=" O GLN E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 Processing helix chain 'E' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU E 582 " --> pdb=" O LYS E 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.604A pdb=" N HIS F 67 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 154 through 160 Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 170 through 181 Processing helix chain 'F' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 266 through 276 Processing helix chain 'F' and resid 291 through 299 Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 311 through 325 removed outlier: 3.826A pdb=" N LYS F 324 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 325 " --> pdb=" O PHE F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'F' and resid 352 through 358 Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA F 388 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.824A pdb=" N ILE F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 434 removed outlier: 3.535A pdb=" N PHE F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 426 " --> pdb=" O THR F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 Processing helix chain 'F' and resid 471 through 479 Processing helix chain 'F' and resid 493 through 509 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY F 523 " --> pdb=" O GLN F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.790A pdb=" N GLU F 582 " --> pdb=" O LYS F 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.605A pdb=" N HIS G 67 " --> pdb=" O TYR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 170 through 181 Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.529A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'G' and resid 266 through 276 Processing helix chain 'G' and resid 291 through 299 Proline residue: G 296 - end of helix Processing helix chain 'G' and resid 311 through 325 removed outlier: 3.825A pdb=" N LYS G 324 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 325 " --> pdb=" O PHE G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 328 No H-bonds generated for 'chain 'G' and resid 326 through 328' Processing helix chain 'G' and resid 341 through 349 Processing helix chain 'G' and resid 352 through 358 Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 373 through 383 Processing helix chain 'G' and resid 384 through 388 removed outlier: 4.094A pdb=" N ALA G 388 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 403 removed outlier: 3.825A pdb=" N ILE G 401 " --> pdb=" O ASP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.534A pdb=" N PHE G 424 " --> pdb=" O GLY G 420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 425 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 426 " --> pdb=" O THR G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 461 Processing helix chain 'G' and resid 471 through 479 Processing helix chain 'G' and resid 493 through 509 Processing helix chain 'G' and resid 518 through 523 removed outlier: 3.512A pdb=" N GLY G 523 " --> pdb=" O GLN G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 550 Processing helix chain 'G' and resid 578 through 583 removed outlier: 3.789A pdb=" N GLU G 582 " --> pdb=" O LYS G 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY A 120 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 6.314A pdb=" N LEU A 204 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 221 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 206 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 219 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP A 208 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL A 260 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP A 307 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU A 262 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 304 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.452A pdb=" N THR G 439 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET G 486 " --> pdb=" O THR G 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP G 441 " --> pdb=" O MET G 486 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 513 " --> pdb=" O THR G 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL G 556 " --> pdb=" O VAL G 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE G 515 " --> pdb=" O VAL G 556 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU G 410 " --> pdb=" O ASN G 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU G 587 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 412 " --> pdb=" O LEU G 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU G 589 " --> pdb=" O VAL G 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR G 414 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP G 591 " --> pdb=" O THR G 414 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN G 622 " --> pdb=" O THR G 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR G 627 " --> pdb=" O ASN G 622 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 622 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 410 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU A 587 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 412 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU A 589 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 414 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP A 591 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 513 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 556 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 515 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR A 439 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET A 486 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP A 441 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY B 120 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU B 204 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 221 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B 206 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 219 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP B 208 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL B 260 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 307 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU B 262 " --> pdb=" O TRP B 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 304 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR B 627 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 622 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 410 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 587 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 412 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU B 589 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 414 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP B 591 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 513 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL B 556 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 515 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 439 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET B 486 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP B 441 " --> pdb=" O MET B 486 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 485 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 368 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY C 120 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU C 204 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU C 221 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 206 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 219 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 208 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL C 260 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP C 307 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU C 262 " --> pdb=" O TRP C 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 304 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 483 through 485 removed outlier: 6.452A pdb=" N THR C 439 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 513 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL C 556 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 515 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 410 " --> pdb=" O ASN C 585 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU C 587 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 412 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 589 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 414 " --> pdb=" O LEU C 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP C 591 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C 622 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 627 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY D 120 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU D 204 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 221 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 206 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D 219 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP D 208 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL D 260 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP D 307 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 262 " --> pdb=" O TRP D 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE D 304 " --> pdb=" O PHE D 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 483 through 485 removed outlier: 6.452A pdb=" N THR D 439 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 513 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL D 556 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 515 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU D 410 " --> pdb=" O ASN D 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU D 587 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 412 " --> pdb=" O LEU D 587 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 589 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 414 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP D 591 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN D 622 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 627 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLY E 120 " --> pdb=" O PHE E 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU E 204 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU E 221 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE E 206 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU E 219 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP E 208 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL E 260 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP E 307 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 262 " --> pdb=" O TRP E 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 304 " --> pdb=" O PHE E 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR E 627 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN E 622 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU E 410 " --> pdb=" O ASN E 585 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU E 587 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL E 412 " --> pdb=" O LEU E 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU E 589 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR E 414 " --> pdb=" O LEU E 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP E 591 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL E 513 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL E 556 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 515 " --> pdb=" O VAL E 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR E 439 " --> pdb=" O TYR E 484 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET E 486 " --> pdb=" O THR E 439 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP E 441 " --> pdb=" O MET E 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY F 120 " --> pdb=" O PHE F 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU F 204 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU F 221 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE F 206 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 219 " --> pdb=" O PHE F 206 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP F 208 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 280 through 282 removed outlier: 6.643A pdb=" N VAL F 260 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP F 307 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU F 262 " --> pdb=" O TRP F 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 304 " --> pdb=" O PHE F 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 627 through 629 removed outlier: 3.645A pdb=" N THR F 627 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 622 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU F 410 " --> pdb=" O ASN F 585 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU F 587 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL F 412 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU F 589 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 414 " --> pdb=" O LEU F 589 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASP F 591 " --> pdb=" O THR F 414 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F 513 " --> pdb=" O THR F 554 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL F 556 " --> pdb=" O VAL F 513 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 515 " --> pdb=" O VAL F 556 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR F 439 " --> pdb=" O TYR F 484 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET F 486 " --> pdb=" O THR F 439 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP F 441 " --> pdb=" O MET F 486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 71 through 72 removed outlier: 3.788A pdb=" N GLY G 120 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 162 through 163 removed outlier: 6.315A pdb=" N LEU G 204 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU G 221 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE G 206 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 219 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP G 208 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 280 through 282 removed outlier: 6.644A pdb=" N VAL G 260 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP G 307 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G 262 " --> pdb=" O TRP G 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE G 304 " --> pdb=" O PHE G 331 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3300 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: 4.94 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9587 1.34 - 1.46: 6823 1.46 - 1.58: 13046 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 29610 Sorted by residual: bond pdb=" C ARG F 199 " pdb=" N PRO F 200 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.25e-01 bond pdb=" C ARG D 199 " pdb=" N PRO D 200 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.08e-01 bond pdb=" C ARG E 199 " pdb=" N PRO E 200 " ideal model delta sigma weight residual 1.335 1.345 -0.009 1.36e-02 5.41e+03 4.59e-01 bond pdb=" C ARG A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.39e-01 bond pdb=" C ARG C 199 " pdb=" N PRO C 200 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.36e-01 ... (remaining 29605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 38878 0.96 - 1.93: 923 1.93 - 2.89: 197 2.89 - 3.86: 70 3.86 - 4.82: 35 Bond angle restraints: 40103 Sorted by residual: angle pdb=" C SER F 447 " pdb=" N ASN F 448 " pdb=" CA ASN F 448 " ideal model delta sigma weight residual 120.38 124.55 -4.17 1.46e+00 4.69e-01 8.16e+00 angle pdb=" C SER C 447 " pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.46e+00 4.69e-01 8.11e+00 angle pdb=" C SER A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta sigma weight residual 120.38 124.53 -4.15 1.46e+00 4.69e-01 8.09e+00 angle pdb=" C SER G 447 " pdb=" N ASN G 448 " pdb=" CA ASN G 448 " ideal model delta sigma weight residual 120.38 124.52 -4.14 1.46e+00 4.69e-01 8.04e+00 angle pdb=" C SER D 447 " pdb=" N ASN D 448 " pdb=" CA ASN D 448 " ideal model delta sigma weight residual 120.38 124.51 -4.13 1.46e+00 4.69e-01 8.02e+00 ... (remaining 40098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 17054 16.61 - 33.23: 523 33.23 - 49.84: 35 49.84 - 66.46: 0 66.46 - 83.07: 7 Dihedral angle restraints: 17619 sinusoidal: 7196 harmonic: 10423 Sorted by residual: dihedral pdb=" N ARG D 202 " pdb=" CA ARG D 202 " pdb=" CB ARG D 202 " pdb=" CG ARG D 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.25 43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" N ARG G 202 " pdb=" CA ARG G 202 " pdb=" CB ARG G 202 " pdb=" CG ARG G 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.24 43.24 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" N ARG B 202 " pdb=" CA ARG B 202 " pdb=" CB ARG B 202 " pdb=" CG ARG B 202 " ideal model delta sinusoidal sigma weight residual -60.00 -103.23 43.23 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 17616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2784 0.026 - 0.052: 1047 0.052 - 0.078: 290 0.078 - 0.104: 214 0.104 - 0.130: 103 Chirality restraints: 4438 Sorted by residual: chirality pdb=" CA ILE C 238 " pdb=" N ILE C 238 " pdb=" C ILE C 238 " pdb=" CB ILE C 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE G 238 " pdb=" N ILE G 238 " pdb=" C ILE G 238 " pdb=" CB ILE G 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 4435 not shown) Planarity restraints: 5187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 199 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.11e-01 pdb=" N PRO G 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO G 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 200 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO A 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.96e-01 pdb=" N PRO F 200 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.013 5.00e-02 4.00e+02 ... (remaining 5184 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9996 2.86 - 3.37: 26536 3.37 - 3.88: 47144 3.88 - 4.39: 52962 4.39 - 4.90: 87777 Nonbonded interactions: 224415 Sorted by model distance: nonbonded pdb=" O LEU D 272 " pdb=" OG1 THR D 276 " model vdw 2.347 3.040 nonbonded pdb=" O LEU A 272 " pdb=" OG1 THR A 276 " model vdw 2.347 3.040 nonbonded pdb=" O LEU E 272 " pdb=" OG1 THR E 276 " model vdw 2.348 3.040 nonbonded pdb=" O LEU F 272 " pdb=" OG1 THR F 276 " model vdw 2.348 3.040 nonbonded pdb=" O LEU B 272 " pdb=" OG1 THR B 276 " model vdw 2.348 3.040 ... (remaining 224410 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.460 Find NCS groups from input model: 0.180 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 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 : 0.001 0.025 29610 Z= 0.078 Angle : 0.416 4.822 40103 Z= 0.222 Chirality : 0.037 0.130 4438 Planarity : 0.003 0.024 5187 Dihedral : 7.595 83.072 10857 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.41 % Allowed : 2.71 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.15), residues: 3521 helix: 1.41 (0.14), residues: 1295 sheet: 0.76 (0.19), residues: 833 loop : -0.45 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 303 TYR 0.004 0.001 TYR B 602 PHE 0.004 0.001 PHE E 111 TRP 0.003 0.001 TRP F 122 HIS 0.002 0.000 HIS E 552 Details of bonding type rmsd covalent geometry : bond 0.00143 (29610) covalent geometry : angle 0.41560 (40103) hydrogen bonds : bond 0.23077 ( 1205) hydrogen bonds : angle 7.21589 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7598 (mtp) cc_final: 0.7170 (mtp) REVERT: A 179 MET cc_start: 0.6924 (ptp) cc_final: 0.5858 (tpt) REVERT: A 204 LEU cc_start: 0.7696 (mt) cc_final: 0.7405 (mp) REVERT: A 206 PHE cc_start: 0.7601 (m-80) cc_final: 0.7376 (m-80) REVERT: A 282 THR cc_start: 0.7186 (p) cc_final: 0.5673 (t) REVERT: A 299 GLU cc_start: 0.6479 (tt0) cc_final: 0.6168 (tt0) REVERT: A 313 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.7068 (tpt-90) REVERT: A 316 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 321 PHE cc_start: 0.7409 (m-10) cc_final: 0.6931 (m-80) REVERT: A 470 LYS cc_start: 0.8373 (mttt) cc_final: 0.8021 (mttt) REVERT: A 496 THR cc_start: 0.7460 (m) cc_final: 0.7163 (p) REVERT: A 501 MET cc_start: 0.8068 (mtp) cc_final: 0.7700 (mtp) REVERT: A 509 ASP cc_start: 0.7104 (m-30) cc_final: 0.5362 (m-30) REVERT: A 610 PHE cc_start: 0.8679 (t80) cc_final: 0.8347 (t80) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.0850 time to fit residues: 13.9315 Evaluate side-chains 112 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.0020 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 0.0870 overall best weight: 0.0248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 HIS ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122732 restraints weight = 9214.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127374 restraints weight = 5940.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130723 restraints weight = 4291.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133118 restraints weight = 3353.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134968 restraints weight = 2780.289| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29610 Z= 0.101 Angle : 0.549 7.920 40103 Z= 0.280 Chirality : 0.041 0.127 4438 Planarity : 0.004 0.029 5187 Dihedral : 3.416 16.414 3941 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.68 (0.15), residues: 3521 helix: 1.34 (0.14), residues: 1295 sheet: 0.59 (0.19), residues: 833 loop : -0.41 (0.18), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 406 TYR 0.012 0.001 TYR E 537 PHE 0.019 0.001 PHE G 520 TRP 0.007 0.001 TRP A 158 HIS 0.004 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00212 (29610) covalent geometry : angle 0.54931 (40103) hydrogen bonds : bond 0.04045 ( 1205) hydrogen bonds : angle 5.42399 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8187 (mp) cc_final: 0.7854 (tp) REVERT: B 79 ARG cc_start: 0.6970 (ptt180) cc_final: 0.6651 (ttp-110) REVERT: B 104 ILE cc_start: 0.8231 (mm) cc_final: 0.7836 (tp) REVERT: B 125 PHE cc_start: 0.8270 (t80) cc_final: 0.7988 (t80) REVERT: B 156 ARG cc_start: 0.8209 (ttt-90) cc_final: 0.7930 (ptm160) REVERT: B 186 THR cc_start: 0.6295 (p) cc_final: 0.5434 (t) REVERT: B 206 PHE cc_start: 0.8339 (m-80) cc_final: 0.8090 (m-80) REVERT: B 283 LEU cc_start: 0.8194 (mt) cc_final: 0.7906 (mt) REVERT: B 285 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7305 (mtt180) REVERT: B 295 LEU cc_start: 0.8269 (mt) cc_final: 0.8025 (mt) REVERT: B 299 GLU cc_start: 0.7074 (tt0) cc_final: 0.6301 (tt0) REVERT: B 304 ILE cc_start: 0.7384 (mt) cc_final: 0.7100 (mp) REVERT: B 316 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 321 PHE cc_start: 0.7936 (m-10) cc_final: 0.7244 (m-10) REVERT: B 323 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7063 (tmm-80) REVERT: B 357 ARG cc_start: 0.7374 (mtm110) cc_final: 0.7024 (mtm110) REVERT: B 423 THR cc_start: 0.6496 (p) cc_final: 0.6243 (t) REVERT: B 451 LEU cc_start: 0.7833 (tp) cc_final: 0.7450 (tp) REVERT: B 455 MET cc_start: 0.7776 (mtp) cc_final: 0.7289 (mtp) REVERT: B 495 ARG cc_start: 0.8673 (tpt90) cc_final: 0.8386 (tpt170) REVERT: B 501 MET cc_start: 0.7992 (mtp) cc_final: 0.7680 (mtp) REVERT: B 509 ASP cc_start: 0.7755 (m-30) cc_final: 0.7140 (m-30) REVERT: B 510 ILE cc_start: 0.8089 (mm) cc_final: 0.7657 (tp) REVERT: B 522 MET cc_start: 0.7939 (mtp) cc_final: 0.7670 (mtp) REVERT: B 543 ARG cc_start: 0.6980 (tpt170) cc_final: 0.6526 (tpt170) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1024 time to fit residues: 15.9717 Evaluate side-chains 109 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 203 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 272 optimal weight: 0.0060 chunk 19 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117677 restraints weight = 9178.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122373 restraints weight = 5900.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125704 restraints weight = 4232.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128168 restraints weight = 3287.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129822 restraints weight = 2696.199| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29610 Z= 0.112 Angle : 0.541 6.275 40103 Z= 0.279 Chirality : 0.041 0.133 4438 Planarity : 0.004 0.037 5187 Dihedral : 3.782 19.938 3941 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.46 (0.15), residues: 3521 helix: 1.18 (0.15), residues: 1309 sheet: 0.40 (0.20), residues: 833 loop : -0.51 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 341 TYR 0.010 0.002 TYR F 428 PHE 0.021 0.001 PHE D 478 TRP 0.011 0.001 TRP B 363 HIS 0.002 0.001 HIS F 512 Details of bonding type rmsd covalent geometry : bond 0.00244 (29610) covalent geometry : angle 0.54095 (40103) hydrogen bonds : bond 0.03507 ( 1205) hydrogen bonds : angle 5.15922 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8199 (mp) cc_final: 0.7963 (tp) REVERT: B 79 ARG cc_start: 0.7109 (ptt180) cc_final: 0.6763 (ptt-90) REVERT: B 105 ASP cc_start: 0.7478 (t0) cc_final: 0.7055 (t0) REVERT: B 110 HIS cc_start: 0.7628 (t70) cc_final: 0.7425 (t70) REVERT: B 125 PHE cc_start: 0.8358 (t80) cc_final: 0.8011 (t80) REVERT: B 152 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5738 (mm-30) REVERT: B 206 PHE cc_start: 0.8349 (m-80) cc_final: 0.8106 (m-80) REVERT: B 283 LEU cc_start: 0.8139 (mt) cc_final: 0.7919 (mt) REVERT: B 285 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7279 (mtt180) REVERT: B 295 LEU cc_start: 0.8548 (mt) cc_final: 0.8252 (mt) REVERT: B 299 GLU cc_start: 0.7102 (tt0) cc_final: 0.6293 (tt0) REVERT: B 304 ILE cc_start: 0.7365 (mt) cc_final: 0.7052 (mp) REVERT: B 307 TRP cc_start: 0.6931 (t60) cc_final: 0.6516 (t60) REVERT: B 313 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7653 (ptm160) REVERT: B 316 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 321 PHE cc_start: 0.8224 (m-10) cc_final: 0.7637 (m-10) REVERT: B 323 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7469 (ttt-90) REVERT: B 324 LYS cc_start: 0.8810 (mttt) cc_final: 0.8480 (mttt) REVERT: B 331 PHE cc_start: 0.7973 (m-80) cc_final: 0.7582 (m-80) REVERT: B 350 PHE cc_start: 0.7148 (t80) cc_final: 0.6865 (t80) REVERT: B 355 ILE cc_start: 0.8471 (mt) cc_final: 0.8076 (mt) REVERT: B 357 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7124 (mtm110) REVERT: B 423 THR cc_start: 0.6822 (p) cc_final: 0.6544 (t) REVERT: B 437 VAL cc_start: 0.6375 (t) cc_final: 0.6083 (p) REVERT: B 451 LEU cc_start: 0.8066 (tp) cc_final: 0.7680 (tp) REVERT: B 453 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8177 (mtp85) REVERT: B 455 MET cc_start: 0.7774 (mtp) cc_final: 0.7342 (mtp) REVERT: B 495 ARG cc_start: 0.8642 (tpt90) cc_final: 0.8431 (tpt170) REVERT: B 496 THR cc_start: 0.8644 (m) cc_final: 0.8429 (p) REVERT: B 509 ASP cc_start: 0.7663 (m-30) cc_final: 0.7043 (m-30) REVERT: B 510 ILE cc_start: 0.8460 (mm) cc_final: 0.8012 (tp) REVERT: B 520 PHE cc_start: 0.7827 (t80) cc_final: 0.7340 (t80) REVERT: B 543 ARG cc_start: 0.7319 (tpt170) cc_final: 0.6605 (tpt170) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0858 time to fit residues: 13.1354 Evaluate side-chains 111 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 355 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 0.0040 chunk 308 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 0.2980 chunk 231 optimal weight: 0.4980 chunk 273 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 291 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118527 restraints weight = 9098.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123239 restraints weight = 5812.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126607 restraints weight = 4192.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128944 restraints weight = 3251.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130841 restraints weight = 2682.258| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29610 Z= 0.102 Angle : 0.532 6.691 40103 Z= 0.272 Chirality : 0.041 0.130 4438 Planarity : 0.003 0.030 5187 Dihedral : 3.697 20.312 3941 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.15), residues: 3521 helix: 1.17 (0.15), residues: 1316 sheet: 0.33 (0.20), residues: 833 loop : -0.50 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 302 TYR 0.014 0.002 TYR F 602 PHE 0.023 0.001 PHE B 478 TRP 0.008 0.001 TRP B 363 HIS 0.002 0.001 HIS E 512 Details of bonding type rmsd covalent geometry : bond 0.00219 (29610) covalent geometry : angle 0.53207 (40103) hydrogen bonds : bond 0.03190 ( 1205) hydrogen bonds : angle 5.08976 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8066 (mp) cc_final: 0.7782 (tp) REVERT: B 105 ASP cc_start: 0.7685 (t0) cc_final: 0.7184 (t0) REVERT: B 110 HIS cc_start: 0.7618 (t70) cc_final: 0.7385 (t70) REVERT: B 125 PHE cc_start: 0.8332 (t80) cc_final: 0.7979 (t80) REVERT: B 152 GLU cc_start: 0.6166 (mm-30) cc_final: 0.5928 (mm-30) REVERT: B 206 PHE cc_start: 0.8360 (m-80) cc_final: 0.8147 (m-80) REVERT: B 285 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7317 (mtt180) REVERT: B 295 LEU cc_start: 0.8609 (mt) cc_final: 0.8357 (mt) REVERT: B 299 GLU cc_start: 0.7060 (tt0) cc_final: 0.6234 (tt0) REVERT: B 304 ILE cc_start: 0.7229 (mt) cc_final: 0.6917 (mp) REVERT: B 313 ARG cc_start: 0.8134 (tmm-80) cc_final: 0.7571 (ptm160) REVERT: B 316 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 321 PHE cc_start: 0.8180 (m-10) cc_final: 0.7556 (m-10) REVERT: B 323 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7608 (ttt-90) REVERT: B 324 LYS cc_start: 0.8787 (mttt) cc_final: 0.8482 (mttt) REVERT: B 331 PHE cc_start: 0.7745 (m-80) cc_final: 0.7224 (m-10) REVERT: B 355 ILE cc_start: 0.8477 (mt) cc_final: 0.8112 (mt) REVERT: B 357 ARG cc_start: 0.7351 (mtm110) cc_final: 0.7097 (mtm110) REVERT: B 392 TRP cc_start: 0.6269 (m-90) cc_final: 0.5967 (m-90) REVERT: B 437 VAL cc_start: 0.6588 (t) cc_final: 0.6302 (p) REVERT: B 451 LEU cc_start: 0.8080 (tp) cc_final: 0.7705 (tp) REVERT: B 453 ARG cc_start: 0.8415 (ttt180) cc_final: 0.8173 (mtp85) REVERT: B 455 MET cc_start: 0.7982 (mtp) cc_final: 0.7563 (mtp) REVERT: B 495 ARG cc_start: 0.8695 (tpt90) cc_final: 0.8444 (tpt170) REVERT: B 509 ASP cc_start: 0.7665 (m-30) cc_final: 0.6836 (m-30) REVERT: B 510 ILE cc_start: 0.8593 (mm) cc_final: 0.8138 (tp) REVERT: B 543 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6532 (tpt170) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0922 time to fit residues: 13.0331 Evaluate side-chains 107 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 0.0060 chunk 347 optimal weight: 0.1980 chunk 197 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 27 optimal weight: 0.0050 chunk 32 optimal weight: 0.0020 overall best weight: 0.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.150309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119088 restraints weight = 9004.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.123913 restraints weight = 5753.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.127069 restraints weight = 4125.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129581 restraints weight = 3251.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131424 restraints weight = 2670.792| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 29610 Z= 0.091 Angle : 0.518 6.754 40103 Z= 0.263 Chirality : 0.041 0.131 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.584 18.066 3941 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.37 (0.15), residues: 3521 helix: 1.07 (0.14), residues: 1316 sheet: 0.38 (0.20), residues: 798 loop : -0.54 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 609 TYR 0.013 0.001 TYR D 602 PHE 0.025 0.001 PHE C 370 TRP 0.005 0.001 TRP B 363 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd covalent geometry : bond 0.00198 (29610) covalent geometry : angle 0.51751 (40103) hydrogen bonds : bond 0.03076 ( 1205) hydrogen bonds : angle 4.94500 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8064 (mp) cc_final: 0.7735 (tp) REVERT: B 79 ARG cc_start: 0.6979 (ptt180) cc_final: 0.6576 (ptt-90) REVERT: B 105 ASP cc_start: 0.7714 (t0) cc_final: 0.7023 (t0) REVERT: B 110 HIS cc_start: 0.7642 (t70) cc_final: 0.7422 (t70) REVERT: B 125 PHE cc_start: 0.8381 (t80) cc_final: 0.8033 (t80) REVERT: B 152 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5906 (mm-30) REVERT: B 206 PHE cc_start: 0.8276 (m-80) cc_final: 0.8023 (m-80) REVERT: B 283 LEU cc_start: 0.8125 (mt) cc_final: 0.7909 (mp) REVERT: B 285 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7191 (mtt180) REVERT: B 295 LEU cc_start: 0.8633 (mt) cc_final: 0.8364 (mt) REVERT: B 299 GLU cc_start: 0.7084 (tt0) cc_final: 0.6286 (tt0) REVERT: B 304 ILE cc_start: 0.7172 (mt) cc_final: 0.6896 (mp) REVERT: B 316 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 321 PHE cc_start: 0.8185 (m-10) cc_final: 0.7520 (m-10) REVERT: B 323 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7668 (ttt-90) REVERT: B 331 PHE cc_start: 0.7586 (m-80) cc_final: 0.7158 (m-10) REVERT: B 355 ILE cc_start: 0.8487 (mt) cc_final: 0.8120 (mt) REVERT: B 357 ARG cc_start: 0.7308 (mtm110) cc_final: 0.7017 (mtm110) REVERT: B 392 TRP cc_start: 0.6353 (m-90) cc_final: 0.6123 (m-90) REVERT: B 437 VAL cc_start: 0.6572 (t) cc_final: 0.6292 (p) REVERT: B 451 LEU cc_start: 0.8092 (tp) cc_final: 0.7751 (tp) REVERT: B 453 ARG cc_start: 0.8420 (ttt180) cc_final: 0.8176 (mtp85) REVERT: B 455 MET cc_start: 0.7976 (mtp) cc_final: 0.7534 (mtp) REVERT: B 495 ARG cc_start: 0.8665 (tpt90) cc_final: 0.8115 (tpt170) REVERT: B 500 THR cc_start: 0.8495 (m) cc_final: 0.8263 (p) REVERT: B 509 ASP cc_start: 0.7659 (m-30) cc_final: 0.6943 (m-30) REVERT: B 510 ILE cc_start: 0.8602 (mm) cc_final: 0.8164 (tp) REVERT: B 522 MET cc_start: 0.7949 (mtt) cc_final: 0.7485 (mtt) REVERT: B 543 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6587 (tpt170) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0792 time to fit residues: 11.1757 Evaluate side-chains 103 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 225 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 280 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 308 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 282 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.146805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115520 restraints weight = 9256.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120230 restraints weight = 5897.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123564 restraints weight = 4258.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125853 restraints weight = 3329.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127806 restraints weight = 2776.064| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 29610 Z= 0.101 Angle : 0.518 7.291 40103 Z= 0.264 Chirality : 0.041 0.127 4438 Planarity : 0.003 0.033 5187 Dihedral : 3.611 19.128 3941 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.48 (0.15), residues: 3521 helix: 1.28 (0.15), residues: 1337 sheet: 0.31 (0.21), residues: 840 loop : -0.57 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.011 0.001 TYR D 602 PHE 0.024 0.001 PHE F 370 TRP 0.006 0.001 TRP F 441 HIS 0.002 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00218 (29610) covalent geometry : angle 0.51798 (40103) hydrogen bonds : bond 0.02942 ( 1205) hydrogen bonds : angle 4.82321 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7991 (mp) cc_final: 0.7730 (tp) REVERT: B 105 ASP cc_start: 0.7725 (t0) cc_final: 0.7095 (t0) REVERT: B 125 PHE cc_start: 0.8416 (t80) cc_final: 0.8065 (t80) REVERT: B 152 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6490 (mm-30) REVERT: B 172 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 206 PHE cc_start: 0.8264 (m-80) cc_final: 0.7915 (m-80) REVERT: B 283 LEU cc_start: 0.7973 (mt) cc_final: 0.7747 (mp) REVERT: B 285 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7331 (mtt180) REVERT: B 295 LEU cc_start: 0.8756 (mt) cc_final: 0.8537 (mt) REVERT: B 299 GLU cc_start: 0.7188 (tt0) cc_final: 0.6414 (tt0) REVERT: B 304 ILE cc_start: 0.7186 (mt) cc_final: 0.6926 (mp) REVERT: B 321 PHE cc_start: 0.8142 (m-10) cc_final: 0.7416 (m-10) REVERT: B 323 ARG cc_start: 0.8432 (ttm170) cc_final: 0.7810 (ttt-90) REVERT: B 331 PHE cc_start: 0.7579 (m-80) cc_final: 0.7198 (m-10) REVERT: B 350 PHE cc_start: 0.6933 (t80) cc_final: 0.6697 (t80) REVERT: B 355 ILE cc_start: 0.8611 (mt) cc_final: 0.8353 (mt) REVERT: B 357 ARG cc_start: 0.7354 (mtm110) cc_final: 0.6944 (mtm180) REVERT: B 360 LEU cc_start: 0.7451 (mt) cc_final: 0.6938 (mt) REVERT: B 370 PHE cc_start: 0.6405 (p90) cc_final: 0.6109 (p90) REVERT: B 437 VAL cc_start: 0.6867 (t) cc_final: 0.6615 (p) REVERT: B 453 ARG cc_start: 0.8536 (ttt180) cc_final: 0.8266 (mtp85) REVERT: B 455 MET cc_start: 0.8131 (mtp) cc_final: 0.7764 (mtp) REVERT: B 483 LEU cc_start: 0.7788 (tp) cc_final: 0.7573 (tp) REVERT: B 495 ARG cc_start: 0.8671 (tpt90) cc_final: 0.8136 (tpt170) REVERT: B 500 THR cc_start: 0.8488 (m) cc_final: 0.8285 (p) REVERT: B 501 MET cc_start: 0.8271 (mtm) cc_final: 0.7900 (mtm) REVERT: B 509 ASP cc_start: 0.7184 (m-30) cc_final: 0.6532 (m-30) REVERT: B 510 ILE cc_start: 0.8551 (mm) cc_final: 0.8154 (tp) REVERT: B 522 MET cc_start: 0.8073 (mtt) cc_final: 0.7844 (mtt) REVERT: B 543 ARG cc_start: 0.7308 (tpt170) cc_final: 0.6979 (tpt170) REVERT: B 544 LYS cc_start: 0.8612 (pttp) cc_final: 0.8311 (pttm) REVERT: B 550 ASN cc_start: 0.8582 (t0) cc_final: 0.8270 (t0) REVERT: B 604 GLN cc_start: 0.7404 (tt0) cc_final: 0.7183 (tp40) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0870 time to fit residues: 13.1086 Evaluate side-chains 115 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 44 optimal weight: 0.7980 chunk 324 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 259 optimal weight: 0.0980 chunk 350 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 319 optimal weight: 0.0980 chunk 272 optimal weight: 0.0030 chunk 155 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 overall best weight: 0.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.149206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.117205 restraints weight = 9131.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121847 restraints weight = 5906.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125322 restraints weight = 4307.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127698 restraints weight = 3390.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129644 restraints weight = 2820.945| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29610 Z= 0.090 Angle : 0.541 8.484 40103 Z= 0.265 Chirality : 0.041 0.130 4438 Planarity : 0.003 0.032 5187 Dihedral : 3.484 16.631 3941 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.15), residues: 3521 helix: 1.33 (0.15), residues: 1288 sheet: 0.45 (0.21), residues: 798 loop : -0.55 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.013 0.001 TYR F 602 PHE 0.020 0.001 PHE G 370 TRP 0.008 0.001 TRP A 158 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd covalent geometry : bond 0.00195 (29610) covalent geometry : angle 0.54062 (40103) hydrogen bonds : bond 0.02821 ( 1205) hydrogen bonds : angle 4.72079 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8005 (mp) cc_final: 0.7694 (tp) REVERT: B 79 ARG cc_start: 0.7014 (ptt180) cc_final: 0.6625 (ptt-90) REVERT: B 105 ASP cc_start: 0.7759 (t0) cc_final: 0.6997 (t0) REVERT: B 125 PHE cc_start: 0.8445 (t80) cc_final: 0.8103 (t80) REVERT: B 152 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6443 (mm-30) REVERT: B 206 PHE cc_start: 0.8218 (m-80) cc_final: 0.7893 (m-80) REVERT: B 283 LEU cc_start: 0.7948 (mt) cc_final: 0.7719 (mt) REVERT: B 285 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7296 (mtt180) REVERT: B 287 THR cc_start: 0.8330 (p) cc_final: 0.8126 (p) REVERT: B 295 LEU cc_start: 0.8739 (mt) cc_final: 0.8528 (mt) REVERT: B 299 GLU cc_start: 0.7074 (tt0) cc_final: 0.6279 (tt0) REVERT: B 304 ILE cc_start: 0.7138 (mt) cc_final: 0.6878 (mp) REVERT: B 321 PHE cc_start: 0.8093 (m-10) cc_final: 0.7501 (m-10) REVERT: B 323 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7869 (ttt-90) REVERT: B 331 PHE cc_start: 0.7538 (m-80) cc_final: 0.7151 (m-10) REVERT: B 355 ILE cc_start: 0.8581 (mt) cc_final: 0.8276 (mt) REVERT: B 357 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7147 (mtm110) REVERT: B 360 LEU cc_start: 0.7380 (mt) cc_final: 0.6874 (mt) REVERT: B 370 PHE cc_start: 0.6376 (p90) cc_final: 0.6086 (p90) REVERT: B 425 ILE cc_start: 0.8525 (tp) cc_final: 0.8325 (tp) REVERT: B 437 VAL cc_start: 0.6811 (t) cc_final: 0.6564 (p) REVERT: B 451 LEU cc_start: 0.8218 (tp) cc_final: 0.7972 (tp) REVERT: B 453 ARG cc_start: 0.8488 (ttt180) cc_final: 0.8235 (mtp85) REVERT: B 455 MET cc_start: 0.8112 (mtp) cc_final: 0.7687 (mtp) REVERT: B 495 ARG cc_start: 0.8656 (tpt90) cc_final: 0.8137 (tpt170) REVERT: B 500 THR cc_start: 0.8533 (m) cc_final: 0.8313 (p) REVERT: B 501 MET cc_start: 0.8257 (mtm) cc_final: 0.7913 (mtm) REVERT: B 509 ASP cc_start: 0.7125 (m-30) cc_final: 0.6550 (m-30) REVERT: B 510 ILE cc_start: 0.8553 (mm) cc_final: 0.8118 (tp) REVERT: B 543 ARG cc_start: 0.7310 (tpt170) cc_final: 0.6457 (tpt170) REVERT: B 550 ASN cc_start: 0.8508 (t0) cc_final: 0.8233 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0775 time to fit residues: 11.5992 Evaluate side-chains 107 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 216 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 0.0170 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 286 optimal weight: 2.9990 chunk 321 optimal weight: 0.2980 chunk 343 optimal weight: 0.0980 chunk 298 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.150259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118279 restraints weight = 9014.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.122987 restraints weight = 5840.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126348 restraints weight = 4235.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128931 restraints weight = 3304.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130788 restraints weight = 2715.901| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29610 Z= 0.091 Angle : 0.533 7.225 40103 Z= 0.266 Chirality : 0.042 0.154 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.585 18.272 3941 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.15), residues: 3521 helix: 1.34 (0.15), residues: 1288 sheet: 0.59 (0.21), residues: 798 loop : -0.62 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 192 TYR 0.013 0.001 TYR E 602 PHE 0.019 0.001 PHE F 370 TRP 0.014 0.001 TRP F 158 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd covalent geometry : bond 0.00199 (29610) covalent geometry : angle 0.53323 (40103) hydrogen bonds : bond 0.02923 ( 1205) hydrogen bonds : angle 4.75879 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8044 (mp) cc_final: 0.7719 (tp) REVERT: B 125 PHE cc_start: 0.8420 (t80) cc_final: 0.8077 (t80) REVERT: B 152 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6453 (mm-30) REVERT: B 206 PHE cc_start: 0.8182 (m-80) cc_final: 0.7845 (m-80) REVERT: B 285 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7240 (mtt180) REVERT: B 299 GLU cc_start: 0.7121 (tt0) cc_final: 0.6383 (tt0) REVERT: B 304 ILE cc_start: 0.7200 (mt) cc_final: 0.6903 (mp) REVERT: B 321 PHE cc_start: 0.8117 (m-10) cc_final: 0.7335 (m-10) REVERT: B 323 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7890 (ttt-90) REVERT: B 324 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8563 (mtmt) REVERT: B 331 PHE cc_start: 0.7554 (m-80) cc_final: 0.7164 (m-10) REVERT: B 355 ILE cc_start: 0.8582 (mt) cc_final: 0.8238 (mt) REVERT: B 357 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7161 (mtm110) REVERT: B 360 LEU cc_start: 0.7498 (mt) cc_final: 0.7010 (mt) REVERT: B 370 PHE cc_start: 0.6742 (p90) cc_final: 0.6520 (p90) REVERT: B 425 ILE cc_start: 0.8609 (tp) cc_final: 0.8408 (tp) REVERT: B 437 VAL cc_start: 0.6929 (t) cc_final: 0.6680 (p) REVERT: B 451 LEU cc_start: 0.8230 (tp) cc_final: 0.7989 (tp) REVERT: B 453 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8225 (mtp85) REVERT: B 455 MET cc_start: 0.8206 (mtp) cc_final: 0.7866 (mtp) REVERT: B 495 ARG cc_start: 0.8705 (tpt90) cc_final: 0.8186 (tpt170) REVERT: B 497 VAL cc_start: 0.8469 (m) cc_final: 0.8059 (m) REVERT: B 500 THR cc_start: 0.8538 (m) cc_final: 0.8314 (p) REVERT: B 501 MET cc_start: 0.8237 (mtm) cc_final: 0.7985 (mtm) REVERT: B 509 ASP cc_start: 0.7692 (m-30) cc_final: 0.7145 (m-30) REVERT: B 510 ILE cc_start: 0.8633 (mm) cc_final: 0.8169 (tp) REVERT: B 522 MET cc_start: 0.8056 (mtm) cc_final: 0.7773 (mtm) REVERT: B 535 GLN cc_start: 0.5857 (tm-30) cc_final: 0.5588 (tm-30) REVERT: B 539 ILE cc_start: 0.8010 (mt) cc_final: 0.7791 (mt) REVERT: B 543 ARG cc_start: 0.7350 (tpt170) cc_final: 0.6521 (tpt170) REVERT: B 550 ASN cc_start: 0.8507 (t0) cc_final: 0.8215 (t0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0894 time to fit residues: 13.7023 Evaluate side-chains 113 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 315 optimal weight: 0.7980 chunk 185 optimal weight: 0.0370 chunk 170 optimal weight: 0.0070 chunk 296 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 64 optimal weight: 0.0000 chunk 141 optimal weight: 0.9980 chunk 317 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 292 optimal weight: 0.0070 chunk 86 optimal weight: 0.0370 overall best weight: 0.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.153940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121898 restraints weight = 9277.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126821 restraints weight = 5993.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130110 restraints weight = 4302.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.132830 restraints weight = 3373.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134579 restraints weight = 2765.554| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29610 Z= 0.096 Angle : 0.555 8.792 40103 Z= 0.276 Chirality : 0.043 0.162 4438 Planarity : 0.003 0.033 5187 Dihedral : 3.592 15.581 3941 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.45 (0.15), residues: 3521 helix: 1.17 (0.15), residues: 1281 sheet: 0.67 (0.21), residues: 798 loop : -0.66 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 406 TYR 0.013 0.001 TYR G 602 PHE 0.017 0.001 PHE D 370 TRP 0.015 0.001 TRP G 392 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd covalent geometry : bond 0.00198 (29610) covalent geometry : angle 0.55486 (40103) hydrogen bonds : bond 0.02984 ( 1205) hydrogen bonds : angle 4.82350 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8669 (mp10) cc_final: 0.8257 (mp10) REVERT: B 69 ILE cc_start: 0.7828 (mp) cc_final: 0.7552 (tp) REVERT: B 105 ASP cc_start: 0.7766 (t0) cc_final: 0.7051 (t0) REVERT: B 125 PHE cc_start: 0.8412 (t80) cc_final: 0.8082 (t80) REVERT: B 206 PHE cc_start: 0.8098 (m-80) cc_final: 0.7815 (m-80) REVERT: B 285 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.7202 (mtp180) REVERT: B 287 THR cc_start: 0.8289 (p) cc_final: 0.8087 (p) REVERT: B 299 GLU cc_start: 0.7214 (tt0) cc_final: 0.6483 (tt0) REVERT: B 304 ILE cc_start: 0.7136 (mt) cc_final: 0.6876 (mp) REVERT: B 321 PHE cc_start: 0.8043 (m-10) cc_final: 0.7372 (m-10) REVERT: B 323 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7809 (ttt-90) REVERT: B 331 PHE cc_start: 0.7563 (m-80) cc_final: 0.7219 (m-10) REVERT: B 360 LEU cc_start: 0.7529 (mt) cc_final: 0.7034 (mt) REVERT: B 370 PHE cc_start: 0.6509 (p90) cc_final: 0.6303 (p90) REVERT: B 383 ASN cc_start: 0.8335 (t0) cc_final: 0.7919 (t0) REVERT: B 437 VAL cc_start: 0.6863 (t) cc_final: 0.6581 (p) REVERT: B 447 SER cc_start: 0.6501 (t) cc_final: 0.6292 (t) REVERT: B 451 LEU cc_start: 0.8204 (tp) cc_final: 0.7713 (tp) REVERT: B 453 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8034 (mtp85) REVERT: B 455 MET cc_start: 0.8223 (mtp) cc_final: 0.7963 (mtp) REVERT: B 470 LYS cc_start: 0.7913 (mttt) cc_final: 0.7652 (mmtt) REVERT: B 495 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8146 (tpt170) REVERT: B 497 VAL cc_start: 0.8539 (m) cc_final: 0.8122 (m) REVERT: B 500 THR cc_start: 0.8542 (m) cc_final: 0.8339 (p) REVERT: B 501 MET cc_start: 0.8286 (mtm) cc_final: 0.8009 (mtm) REVERT: B 509 ASP cc_start: 0.7716 (m-30) cc_final: 0.6992 (m-30) REVERT: B 510 ILE cc_start: 0.8572 (mm) cc_final: 0.8144 (tp) REVERT: B 522 MET cc_start: 0.7945 (mtm) cc_final: 0.7736 (mtm) REVERT: B 539 ILE cc_start: 0.7991 (mt) cc_final: 0.7769 (mt) REVERT: B 543 ARG cc_start: 0.7425 (tpt170) cc_final: 0.6791 (tpt170) REVERT: B 548 ASP cc_start: 0.7863 (m-30) cc_final: 0.7656 (m-30) REVERT: B 550 ASN cc_start: 0.8457 (t0) cc_final: 0.8257 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0949 time to fit residues: 14.6688 Evaluate side-chains 111 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 294 optimal weight: 0.3980 chunk 170 optimal weight: 1.9990 chunk 230 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 179 optimal weight: 0.0870 chunk 221 optimal weight: 0.0070 chunk 107 optimal weight: 0.0980 overall best weight: 0.1354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.121014 restraints weight = 9158.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125851 restraints weight = 5998.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129278 restraints weight = 4384.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.131761 restraints weight = 3456.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.133623 restraints weight = 2872.701| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 29610 Z= 0.093 Angle : 0.539 5.938 40103 Z= 0.269 Chirality : 0.042 0.160 4438 Planarity : 0.003 0.033 5187 Dihedral : 3.588 16.930 3941 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.15), residues: 3521 helix: 1.08 (0.15), residues: 1295 sheet: 0.73 (0.21), residues: 798 loop : -0.65 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.014 0.001 TYR C 602 PHE 0.018 0.001 PHE B 370 TRP 0.017 0.001 TRP G 392 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd covalent geometry : bond 0.00203 (29610) covalent geometry : angle 0.53862 (40103) hydrogen bonds : bond 0.03078 ( 1205) hydrogen bonds : angle 4.76213 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8670 (mp10) cc_final: 0.8256 (mp10) REVERT: B 69 ILE cc_start: 0.7871 (mp) cc_final: 0.7560 (tp) REVERT: B 105 ASP cc_start: 0.7750 (t0) cc_final: 0.6735 (t0) REVERT: B 125 PHE cc_start: 0.8426 (t80) cc_final: 0.8089 (t80) REVERT: B 285 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.6877 (mmm-85) REVERT: B 287 THR cc_start: 0.8250 (p) cc_final: 0.8005 (p) REVERT: B 299 GLU cc_start: 0.7174 (tt0) cc_final: 0.6621 (tt0) REVERT: B 304 ILE cc_start: 0.7148 (mt) cc_final: 0.6849 (mp) REVERT: B 321 PHE cc_start: 0.8103 (m-10) cc_final: 0.7516 (m-10) REVERT: B 323 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7916 (ttt-90) REVERT: B 355 ILE cc_start: 0.8487 (mt) cc_final: 0.8123 (mt) REVERT: B 356 LEU cc_start: 0.8621 (pp) cc_final: 0.8416 (pp) REVERT: B 357 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7135 (mtm110) REVERT: B 360 LEU cc_start: 0.7542 (mt) cc_final: 0.7078 (mt) REVERT: B 406 ARG cc_start: 0.7653 (mmt-90) cc_final: 0.7242 (mmt90) REVERT: B 425 ILE cc_start: 0.8584 (tp) cc_final: 0.8383 (tp) REVERT: B 437 VAL cc_start: 0.6912 (t) cc_final: 0.6693 (p) REVERT: B 451 LEU cc_start: 0.8164 (tp) cc_final: 0.7946 (tp) REVERT: B 455 MET cc_start: 0.8246 (mtp) cc_final: 0.7981 (mtp) REVERT: B 470 LYS cc_start: 0.7942 (mttt) cc_final: 0.7675 (mmtt) REVERT: B 495 ARG cc_start: 0.8708 (tpt90) cc_final: 0.8187 (tpt170) REVERT: B 497 VAL cc_start: 0.8527 (m) cc_final: 0.8137 (m) REVERT: B 500 THR cc_start: 0.8565 (m) cc_final: 0.8363 (p) REVERT: B 501 MET cc_start: 0.8276 (mtm) cc_final: 0.8000 (mtm) REVERT: B 509 ASP cc_start: 0.7735 (m-30) cc_final: 0.7103 (m-30) REVERT: B 510 ILE cc_start: 0.8633 (mm) cc_final: 0.8245 (tp) REVERT: B 522 MET cc_start: 0.8002 (mtm) cc_final: 0.7717 (mtm) REVERT: B 543 ARG cc_start: 0.7476 (tpt170) cc_final: 0.6612 (tpt170) REVERT: B 550 ASN cc_start: 0.8469 (t0) cc_final: 0.8176 (t0) REVERT: B 591 ASP cc_start: 0.4846 (m-30) cc_final: 0.3098 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0959 time to fit residues: 14.4239 Evaluate side-chains 111 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 315 optimal weight: 3.9990 chunk 352 optimal weight: 0.0000 chunk 296 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 306 optimal weight: 6.9990 chunk 192 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.151214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118390 restraints weight = 9009.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.123083 restraints weight = 5870.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126442 restraints weight = 4281.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128977 restraints weight = 3381.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130897 restraints weight = 2801.882| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29610 Z= 0.103 Angle : 0.562 7.140 40103 Z= 0.288 Chirality : 0.042 0.143 4438 Planarity : 0.003 0.033 5187 Dihedral : 3.681 16.038 3941 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.35 (0.15), residues: 3521 helix: 1.16 (0.15), residues: 1330 sheet: 0.74 (0.20), residues: 791 loop : -0.94 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.009 0.001 TYR B 428 PHE 0.025 0.002 PHE C 370 TRP 0.013 0.001 TRP B 392 HIS 0.003 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00231 (29610) covalent geometry : angle 0.56212 (40103) hydrogen bonds : bond 0.03026 ( 1205) hydrogen bonds : angle 4.77936 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.08 seconds wall clock time: 36 minutes 22.86 seconds (2182.86 seconds total)