Starting phenix.real_space_refine on Mon Sep 14 07:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8c_25744/09_2026/7t8c_25744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8c_25744/09_2026/7t8c_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_25744/09_2026/7t8c_25744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8c_25744/09_2026/7t8c_25744.map" model { file = "/net/cci-nas-00/data/ceres_data/7t8c_25744/09_2026/7t8c_25744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8c_25744/09_2026/7t8c_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.53, per 1000 atoms: 0.19 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: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.12 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: 6.50 Time building geometry restraints manager: 3.35 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: 0.10 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: 6.610 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.900 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 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 are 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/Z covalent geometry : bond 0.00143 / 0.08 (29610) covalent geometry : angle 0.41560 / 0.22 (40103) hydrogen bonds : bond 0.23077 / 15.33 ( 1205) hydrogen bonds : angle 7.21589 / 5.08 ( 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 : 0.144 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: 0.6480 (tt0) cc_final: 0.6169 (tt0) REVERT: A 313 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.7068 (tpt-90) REVERT: A 316 GLU cc_start: 0.7937 (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: 0.1020 time to fit residues: 16.8708 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 : 0.153 ------------------------------------------------------------------------------- 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... A 503 HIS ** A 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 = 0.4171 r_free = 0.4171 target = 0.154389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122487 restraints weight = 9234.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127074 restraints weight = 5953.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130405 restraints weight = 4296.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.132850 restraints weight = 3348.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134752 restraints weight = 2775.523| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.2923 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 are 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/Z covalent geometry : bond 0.00212 / 0.10 (29610) covalent geometry : angle 0.54931 / 0.28 (40103) hydrogen bonds : bond 0.04045 / 2.83 ( 1205) hydrogen bonds : angle 5.42399 / 3.82 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 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 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8187 (mp) cc_final: 0.7860 (tp) REVERT: B 79 ARG cc_start: 0.6962 (ptt180) cc_final: 0.6646 (ttp-110) REVERT: B 104 ILE cc_start: 0.8228 (mm) cc_final: 0.7837 (tp) REVERT: B 125 PHE cc_start: 0.8257 (t80) cc_final: 0.7977 (t80) REVERT: B 156 ARG cc_start: 0.8204 (ttt-90) cc_final: 0.7923 (ptm160) REVERT: B 186 THR cc_start: 0.6293 (p) cc_final: 0.5429 (t) REVERT: B 206 PHE cc_start: 0.8341 (m-80) cc_final: 0.8092 (m-80) REVERT: B 283 LEU cc_start: 0.8194 (mt) cc_final: 0.7905 (mt) REVERT: B 285 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7302 (mtt180) REVERT: B 295 LEU cc_start: 0.8275 (mt) cc_final: 0.8031 (mt) REVERT: B 299 GLU cc_start: 0.7080 (tt0) cc_final: 0.6310 (tt0) REVERT: B 304 ILE cc_start: 0.7389 (mt) cc_final: 0.7105 (mp) REVERT: B 316 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 321 PHE cc_start: 0.7930 (m-10) cc_final: 0.7237 (m-10) REVERT: B 323 ARG cc_start: 0.7727 (ttm170) cc_final: 0.7052 (tmm-80) REVERT: B 357 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7026 (mtm110) REVERT: B 423 THR cc_start: 0.6498 (p) cc_final: 0.6247 (t) REVERT: B 451 LEU cc_start: 0.7830 (tp) cc_final: 0.7447 (tp) REVERT: B 455 MET cc_start: 0.7778 (mtp) cc_final: 0.7287 (mtp) REVERT: B 495 ARG cc_start: 0.8680 (tpt90) cc_final: 0.8392 (tpt170) REVERT: B 501 MET cc_start: 0.7990 (mtp) cc_final: 0.7681 (mtp) REVERT: B 509 ASP cc_start: 0.7751 (m-30) cc_final: 0.7138 (m-30) REVERT: B 510 ILE cc_start: 0.8087 (mm) cc_final: 0.7657 (tp) REVERT: B 522 MET cc_start: 0.7931 (mtp) cc_final: 0.7662 (mtp) REVERT: B 543 ARG cc_start: 0.6979 (tpt170) cc_final: 0.6522 (tpt170) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0914 time to fit residues: 14.2795 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 : 0.173 ------------------------------------------------------------------------------- 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: 0.0070 chunk 245 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 54 optimal weight: 0.0980 chunk 338 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 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 = 0.4193 r_free = 0.4193 target = 0.156022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122631 restraints weight = 9433.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127810 restraints weight = 6099.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.131396 restraints weight = 4358.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134070 restraints weight = 3376.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.135874 restraints weight = 2768.070| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29610 Z= 0.098 Angle : 0.530 6.574 40103 Z= 0.271 Chirality : 0.041 0.132 4438 Planarity : 0.004 0.040 5187 Dihedral : 3.682 19.108 3941 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 are not related in a simple way. whole: 0.57 (0.15), residues: 3521 helix: 1.19 (0.15), residues: 1309 sheet: 0.58 (0.20), residues: 833 loop : -0.45 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.010 0.001 TYR B 428 PHE 0.023 0.001 PHE D 478 TRP 0.007 0.001 TRP B 363 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (29610) covalent geometry : angle 0.52977 / 0.27 (40103) hydrogen bonds : bond 0.03530 / 2.46 ( 1205) hydrogen bonds : angle 5.12469 / 3.61 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 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 126 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8344 (mp) cc_final: 0.8027 (tp) REVERT: B 79 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6634 (ptt-90) REVERT: B 125 PHE cc_start: 0.8246 (t80) cc_final: 0.7951 (t80) REVERT: B 152 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5594 (mm-30) REVERT: B 285 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7159 (mtt180) REVERT: B 290 LEU cc_start: 0.8667 (tp) cc_final: 0.8417 (tt) REVERT: B 304 ILE cc_start: 0.7346 (mt) cc_final: 0.7024 (mp) REVERT: B 307 TRP cc_start: 0.6616 (t60) cc_final: 0.6261 (t60) REVERT: B 313 ARG cc_start: 0.7972 (tmm-80) cc_final: 0.7595 (tmm-80) REVERT: B 316 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 321 PHE cc_start: 0.8107 (m-10) cc_final: 0.7620 (m-10) REVERT: B 324 LYS cc_start: 0.8836 (mttt) cc_final: 0.8559 (mttt) REVERT: B 331 PHE cc_start: 0.7849 (m-80) cc_final: 0.7623 (m-80) REVERT: B 350 PHE cc_start: 0.7056 (t80) cc_final: 0.6738 (t80) REVERT: B 357 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6957 (mtm110) REVERT: B 453 ARG cc_start: 0.8353 (ttt180) cc_final: 0.8126 (mtp85) REVERT: B 455 MET cc_start: 0.7723 (mtp) cc_final: 0.7361 (mtp) REVERT: B 496 THR cc_start: 0.8656 (m) cc_final: 0.8402 (p) REVERT: B 509 ASP cc_start: 0.7725 (m-30) cc_final: 0.7134 (m-30) REVERT: B 510 ILE cc_start: 0.8122 (mm) cc_final: 0.7786 (tp) REVERT: B 520 PHE cc_start: 0.7832 (t80) cc_final: 0.7106 (t80) REVERT: B 522 MET cc_start: 0.8039 (mtp) cc_final: 0.7640 (mtp) REVERT: B 543 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6556 (tpt170) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0892 time to fit residues: 13.5993 Evaluate side-chains 101 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 0.4980 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 231 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.0205 > 50:) chunk 273 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 291 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.147103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116405 restraints weight = 8998.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121086 restraints weight = 5724.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124604 restraints weight = 4085.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126905 restraints weight = 3144.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.128825 restraints weight = 2596.759| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29610 Z= 0.121 Angle : 0.548 6.499 40103 Z= 0.285 Chirality : 0.042 0.132 4438 Planarity : 0.004 0.033 5187 Dihedral : 3.905 20.264 3941 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 are not related in a simple way. whole: 0.54 (0.15), residues: 3521 helix: 1.33 (0.15), residues: 1351 sheet: 0.20 (0.19), residues: 875 loop : -0.45 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 199 TYR 0.014 0.002 TYR B 602 PHE 0.025 0.002 PHE E 370 TRP 0.011 0.001 TRP B 363 HIS 0.004 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (29610) covalent geometry : angle 0.54779 / 0.29 (40103) hydrogen bonds : bond 0.03303 / 2.29 ( 1205) hydrogen bonds : angle 5.19957 / 3.65 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 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 121 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8044 (mp) cc_final: 0.7758 (tp) REVERT: B 79 ARG cc_start: 0.7003 (ptt180) cc_final: 0.6584 (ptt-90) REVERT: B 105 ASP cc_start: 0.7587 (t0) cc_final: 0.7140 (t0) REVERT: B 125 PHE cc_start: 0.8365 (t80) cc_final: 0.8022 (t80) REVERT: B 152 GLU cc_start: 0.6313 (mm-30) cc_final: 0.6072 (mm-30) REVERT: B 206 PHE cc_start: 0.8485 (m-80) cc_final: 0.8134 (m-80) REVERT: B 285 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7478 (mtt180) REVERT: B 295 LEU cc_start: 0.8706 (mt) cc_final: 0.8482 (mt) REVERT: B 299 GLU cc_start: 0.7227 (tt0) cc_final: 0.6694 (tt0) REVERT: B 304 ILE cc_start: 0.7360 (mt) cc_final: 0.7054 (mp) REVERT: B 313 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.7828 (ptm160) REVERT: B 316 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 321 PHE cc_start: 0.8271 (m-10) cc_final: 0.7644 (m-10) REVERT: B 324 LYS cc_start: 0.8760 (mttt) cc_final: 0.8534 (mttt) REVERT: B 331 PHE cc_start: 0.7792 (m-80) cc_final: 0.7372 (m-10) REVERT: B 355 ILE cc_start: 0.8492 (mt) cc_final: 0.8204 (mt) REVERT: B 357 ARG cc_start: 0.7346 (mtm110) cc_final: 0.7000 (mtm110) REVERT: B 437 VAL cc_start: 0.6802 (t) cc_final: 0.6540 (p) REVERT: B 453 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8225 (mtp85) REVERT: B 455 MET cc_start: 0.7996 (mtp) cc_final: 0.7792 (mtp) REVERT: B 470 LYS cc_start: 0.8223 (mttt) cc_final: 0.8003 (mttt) REVERT: B 495 ARG cc_start: 0.8703 (tpt170) cc_final: 0.8482 (tpt170) REVERT: B 509 ASP cc_start: 0.7688 (m-30) cc_final: 0.6776 (m-30) REVERT: B 510 ILE cc_start: 0.8661 (mm) cc_final: 0.8400 (tp) REVERT: B 522 MET cc_start: 0.8160 (mtp) cc_final: 0.7822 (mtp) REVERT: B 588 ILE cc_start: 0.7723 (mp) cc_final: 0.7521 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0835 time to fit residues: 12.3571 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 : 0.152 ------------------------------------------------------------------------------- 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: 2.9990 chunk 239 optimal weight: 0.7980 chunk 347 optimal weight: 0.5980 chunk 197 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 127 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4095 r_free = 0.4095 target = 0.148220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117478 restraints weight = 8916.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122033 restraints weight = 5718.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125329 restraints weight = 4146.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127732 restraints weight = 3240.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129404 restraints weight = 2660.411| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29610 Z= 0.101 Angle : 0.545 10.174 40103 Z= 0.276 Chirality : 0.042 0.129 4438 Planarity : 0.003 0.030 5187 Dihedral : 3.764 18.437 3941 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 are not related in a simple way. whole: 0.47 (0.15), residues: 3521 helix: 1.11 (0.14), residues: 1358 sheet: 0.52 (0.20), residues: 798 loop : -0.54 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.012 0.001 TYR G 602 PHE 0.025 0.001 PHE A 370 TRP 0.008 0.001 TRP G 363 HIS 0.002 0.000 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (29610) covalent geometry : angle 0.54505 / 0.28 (40103) hydrogen bonds : bond 0.03242 / 2.27 ( 1205) hydrogen bonds : angle 5.05348 / 3.53 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 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 121 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7895 (mp) cc_final: 0.7615 (tp) REVERT: B 79 ARG cc_start: 0.7011 (ptt180) cc_final: 0.6600 (ptt-90) REVERT: B 105 ASP cc_start: 0.7688 (t0) cc_final: 0.7249 (t0) REVERT: B 125 PHE cc_start: 0.8399 (t80) cc_final: 0.8029 (t80) REVERT: B 152 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6334 (mm-30) REVERT: B 206 PHE cc_start: 0.8373 (m-80) cc_final: 0.7942 (m-80) REVERT: B 285 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7508 (mtt180) REVERT: B 295 LEU cc_start: 0.8763 (mt) cc_final: 0.8543 (mt) REVERT: B 299 GLU cc_start: 0.7291 (tt0) cc_final: 0.6782 (tt0) REVERT: B 304 ILE cc_start: 0.7300 (mt) cc_final: 0.7041 (mp) REVERT: B 321 PHE cc_start: 0.8351 (m-10) cc_final: 0.7683 (m-10) REVERT: B 324 LYS cc_start: 0.8759 (mttt) cc_final: 0.8508 (mttt) REVERT: B 331 PHE cc_start: 0.7603 (m-80) cc_final: 0.7271 (m-10) REVERT: B 355 ILE cc_start: 0.8573 (mt) cc_final: 0.8210 (mt) REVERT: B 356 LEU cc_start: 0.8556 (pp) cc_final: 0.8350 (pp) REVERT: B 357 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7045 (mtm110) REVERT: B 360 LEU cc_start: 0.7402 (mt) cc_final: 0.6893 (mt) REVERT: B 425 ILE cc_start: 0.8499 (tp) cc_final: 0.8207 (tp) REVERT: B 437 VAL cc_start: 0.6992 (t) cc_final: 0.6674 (p) REVERT: B 443 SER cc_start: 0.7208 (m) cc_final: 0.6534 (m) REVERT: B 451 LEU cc_start: 0.8199 (tp) cc_final: 0.7868 (tp) REVERT: B 453 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8180 (mtp85) REVERT: B 455 MET cc_start: 0.8005 (mtp) cc_final: 0.7755 (mtp) REVERT: B 495 ARG cc_start: 0.8634 (tpt170) cc_final: 0.8434 (tpt170) REVERT: B 501 MET cc_start: 0.8259 (mtm) cc_final: 0.7816 (mtm) REVERT: B 509 ASP cc_start: 0.7610 (m-30) cc_final: 0.6734 (m-30) REVERT: B 510 ILE cc_start: 0.8581 (mm) cc_final: 0.8267 (tp) REVERT: B 522 MET cc_start: 0.8151 (mtp) cc_final: 0.7908 (mtp) REVERT: B 604 GLN cc_start: 0.7463 (tt0) cc_final: 0.7098 (tp40) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0808 time to fit residues: 12.0490 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 : 0.171 ------------------------------------------------------------------------------- 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: 0.6980 chunk 280 optimal weight: 0.9980 chunk 69 optimal weight: 0.0770 chunk 308 optimal weight: 0.0270 chunk 306 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 282 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 HIS B 174 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116117 restraints weight = 9053.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120795 restraints weight = 5918.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124189 restraints weight = 4301.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126771 restraints weight = 3347.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128684 restraints weight = 2743.645| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.5963 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= 0.096 Angle : 0.542 8.536 40103 Z= 0.273 Chirality : 0.042 0.151 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.741 18.315 3941 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 are not related in a simple way. whole: 0.51 (0.15), residues: 3521 helix: 1.23 (0.15), residues: 1358 sheet: 0.45 (0.20), residues: 840 loop : -0.59 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 202 TYR 0.012 0.001 TYR D 602 PHE 0.023 0.001 PHE G 370 TRP 0.008 0.001 TRP G 441 HIS 0.002 0.001 HIS G 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (29610) covalent geometry : angle 0.54168 / 0.27 (40103) hydrogen bonds : bond 0.03131 / 2.21 ( 1205) hydrogen bonds : angle 4.93356 / 3.45 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 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 119 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7951 (mp) cc_final: 0.7696 (tp) REVERT: B 79 ARG cc_start: 0.6969 (ptt180) cc_final: 0.6562 (ptt-90) REVERT: B 125 PHE cc_start: 0.8390 (t80) cc_final: 0.8030 (t80) REVERT: B 152 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6480 (mm-30) REVERT: B 206 PHE cc_start: 0.8331 (m-80) cc_final: 0.7892 (m-80) REVERT: B 283 LEU cc_start: 0.8069 (mt) cc_final: 0.7845 (mp) REVERT: B 285 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7393 (mtt180) REVERT: B 299 GLU cc_start: 0.7355 (tt0) cc_final: 0.6825 (tt0) REVERT: B 304 ILE cc_start: 0.7319 (mt) cc_final: 0.7063 (mp) REVERT: B 306 PHE cc_start: 0.7879 (m-80) cc_final: 0.7423 (m-80) REVERT: B 321 PHE cc_start: 0.8387 (m-10) cc_final: 0.7509 (m-10) REVERT: B 323 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7984 (mmm-85) REVERT: B 331 PHE cc_start: 0.7591 (m-80) cc_final: 0.7251 (m-10) REVERT: B 355 ILE cc_start: 0.8594 (mt) cc_final: 0.8249 (mt) REVERT: B 356 LEU cc_start: 0.8549 (pp) cc_final: 0.8344 (pp) REVERT: B 357 ARG cc_start: 0.7382 (mtm110) cc_final: 0.7031 (mtm110) REVERT: B 360 LEU cc_start: 0.7440 (mt) cc_final: 0.6961 (mt) REVERT: B 370 PHE cc_start: 0.6361 (p90) cc_final: 0.6048 (p90) REVERT: B 437 VAL cc_start: 0.7043 (t) cc_final: 0.6736 (p) REVERT: B 453 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8218 (mtp85) REVERT: B 455 MET cc_start: 0.8169 (mtp) cc_final: 0.7777 (mtp) REVERT: B 495 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8228 (tpt90) REVERT: B 501 MET cc_start: 0.8295 (mtm) cc_final: 0.7859 (mtm) REVERT: B 509 ASP cc_start: 0.7530 (m-30) cc_final: 0.6671 (m-30) REVERT: B 510 ILE cc_start: 0.8521 (mm) cc_final: 0.8278 (tp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0856 time to fit residues: 12.4167 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 : 0.148 ------------------------------------------------------------------------------- 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: 0.5980 chunk 324 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 319 optimal weight: 0.0040 chunk 272 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 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 = 0.4091 r_free = 0.4091 target = 0.147296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115779 restraints weight = 9146.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120374 restraints weight = 5945.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.123704 restraints weight = 4314.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126124 restraints weight = 3372.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127786 restraints weight = 2780.162| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 29610 Z= 0.101 Angle : 0.538 7.344 40103 Z= 0.272 Chirality : 0.042 0.142 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.824 18.047 3941 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 are not related in a simple way. whole: 0.51 (0.15), residues: 3521 helix: 1.35 (0.15), residues: 1323 sheet: 0.58 (0.21), residues: 798 loop : -0.74 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 323 TYR 0.012 0.001 TYR D 602 PHE 0.021 0.001 PHE F 370 TRP 0.009 0.001 TRP G 158 HIS 0.002 0.001 HIS C 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (29610) covalent geometry : angle 0.53800 / 0.27 (40103) hydrogen bonds : bond 0.03132 / 2.22 ( 1205) hydrogen bonds : angle 4.89840 / 3.43 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 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 119 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7988 (mp) cc_final: 0.7676 (tp) REVERT: B 79 ARG cc_start: 0.6967 (ptt180) cc_final: 0.6698 (ttp-110) REVERT: B 125 PHE cc_start: 0.8419 (t80) cc_final: 0.8036 (t80) REVERT: B 152 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6615 (mm-30) REVERT: B 206 PHE cc_start: 0.8287 (m-80) cc_final: 0.7821 (m-80) REVERT: B 252 LEU cc_start: 0.8831 (tt) cc_final: 0.8052 (mt) REVERT: B 283 LEU cc_start: 0.7954 (mt) cc_final: 0.7740 (mp) REVERT: B 285 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7348 (mtt180) REVERT: B 299 GLU cc_start: 0.7422 (tt0) cc_final: 0.6996 (tt0) REVERT: B 304 ILE cc_start: 0.7227 (mt) cc_final: 0.6975 (mp) REVERT: B 306 PHE cc_start: 0.8015 (m-80) cc_final: 0.7255 (m-80) REVERT: B 321 PHE cc_start: 0.8262 (m-10) cc_final: 0.7393 (m-10) REVERT: B 323 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7886 (mmm-85) REVERT: B 331 PHE cc_start: 0.7488 (m-80) cc_final: 0.7190 (m-10) REVERT: B 333 VAL cc_start: 0.8627 (t) cc_final: 0.8191 (m) REVERT: B 360 LEU cc_start: 0.7595 (mt) cc_final: 0.7151 (mt) REVERT: B 437 VAL cc_start: 0.7159 (t) cc_final: 0.6868 (p) REVERT: B 453 ARG cc_start: 0.8491 (ttt180) cc_final: 0.8170 (ptm160) REVERT: B 455 MET cc_start: 0.8219 (mtp) cc_final: 0.7940 (mtp) REVERT: B 495 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8207 (tpt90) REVERT: B 497 VAL cc_start: 0.8735 (m) cc_final: 0.8342 (m) REVERT: B 501 MET cc_start: 0.8300 (mtm) cc_final: 0.7966 (mtm) REVERT: B 509 ASP cc_start: 0.7232 (m-30) cc_final: 0.6641 (m-30) REVERT: B 510 ILE cc_start: 0.8449 (mm) cc_final: 0.8055 (mm) REVERT: B 544 LYS cc_start: 0.8596 (pttp) cc_final: 0.8358 (pttm) REVERT: B 604 GLN cc_start: 0.7464 (tt0) cc_final: 0.7092 (tm-30) REVERT: B 610 PHE cc_start: 0.8433 (t80) cc_final: 0.7782 (t80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0940 time to fit residues: 13.4146 Evaluate side-chains 104 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 0.8980 chunk 90 optimal weight: 0.2980 chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 321 optimal weight: 0.0980 chunk 343 optimal weight: 0.3980 chunk 298 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.149257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116960 restraints weight = 8824.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121353 restraints weight = 5826.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124484 restraints weight = 4322.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126912 restraints weight = 3447.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128710 restraints weight = 2877.718| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.6853 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= 0.099 Angle : 0.588 8.254 40103 Z= 0.292 Chirality : 0.043 0.163 4438 Planarity : 0.003 0.028 5187 Dihedral : 3.819 17.904 3941 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.02 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 are not related in a simple way. whole: 0.42 (0.15), residues: 3521 helix: 1.16 (0.15), residues: 1281 sheet: 0.56 (0.20), residues: 805 loop : -0.63 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.012 0.001 TYR G 602 PHE 0.022 0.001 PHE A 370 TRP 0.013 0.001 TRP C 392 HIS 0.004 0.001 HIS G 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (29610) covalent geometry : angle 0.58824 / 0.29 (40103) hydrogen bonds : bond 0.03165 / 2.23 ( 1205) hydrogen bonds : angle 4.91600 / 3.43 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 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 119 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7797 (mp) cc_final: 0.7567 (tp) REVERT: B 79 ARG cc_start: 0.6952 (ptt180) cc_final: 0.6730 (ttp-110) REVERT: B 125 PHE cc_start: 0.8417 (t80) cc_final: 0.8032 (t80) REVERT: B 152 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6643 (mm-30) REVERT: B 184 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7315 (mmmt) REVERT: B 206 PHE cc_start: 0.8216 (m-80) cc_final: 0.7771 (m-80) REVERT: B 248 PHE cc_start: 0.7571 (t80) cc_final: 0.7270 (t80) REVERT: B 252 LEU cc_start: 0.8814 (tt) cc_final: 0.7900 (mt) REVERT: B 283 LEU cc_start: 0.7923 (mt) cc_final: 0.7699 (mp) REVERT: B 285 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7264 (mtt-85) REVERT: B 299 GLU cc_start: 0.7389 (tt0) cc_final: 0.6815 (tt0) REVERT: B 304 ILE cc_start: 0.7205 (mt) cc_final: 0.6930 (mp) REVERT: B 306 PHE cc_start: 0.7918 (m-80) cc_final: 0.7085 (m-80) REVERT: B 321 PHE cc_start: 0.8275 (m-10) cc_final: 0.7407 (m-10) REVERT: B 323 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7932 (mmm-85) REVERT: B 324 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8609 (mtmt) REVERT: B 331 PHE cc_start: 0.7510 (m-80) cc_final: 0.7282 (m-10) REVERT: B 332 LEU cc_start: 0.7486 (mt) cc_final: 0.7264 (mt) REVERT: B 333 VAL cc_start: 0.8566 (t) cc_final: 0.8139 (m) REVERT: B 355 ILE cc_start: 0.8525 (mt) cc_final: 0.8208 (mt) REVERT: B 357 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7111 (mtm110) REVERT: B 360 LEU cc_start: 0.7495 (mt) cc_final: 0.6971 (mt) REVERT: B 370 PHE cc_start: 0.6436 (p90) cc_final: 0.6168 (p90) REVERT: B 437 VAL cc_start: 0.7133 (t) cc_final: 0.6887 (p) REVERT: B 455 MET cc_start: 0.8302 (mtp) cc_final: 0.8048 (mtp) REVERT: B 495 ARG cc_start: 0.8616 (tpt170) cc_final: 0.8207 (tpt90) REVERT: B 501 MET cc_start: 0.8283 (mtm) cc_final: 0.7857 (mtm) REVERT: B 509 ASP cc_start: 0.7501 (m-30) cc_final: 0.7193 (m-30) REVERT: B 510 ILE cc_start: 0.8548 (mm) cc_final: 0.8181 (mm) REVERT: B 513 VAL cc_start: 0.7852 (t) cc_final: 0.7634 (t) REVERT: B 522 MET cc_start: 0.7920 (mtt) cc_final: 0.7381 (mtt) REVERT: B 591 ASP cc_start: 0.5362 (m-30) cc_final: 0.4325 (t70) REVERT: B 604 GLN cc_start: 0.7458 (tt0) cc_final: 0.7079 (tm-30) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0887 time to fit residues: 12.7898 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.9990 chunk 185 optimal weight: 0.0970 chunk 170 optimal weight: 0.0870 chunk 296 optimal weight: 0.9980 chunk 253 optimal weight: 0.5980 chunk 64 optimal weight: 0.0030 chunk 141 optimal weight: 0.3980 chunk 317 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 292 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 overall best weight: 0.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** B 386 GLN ** 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 = 0.4127 r_free = 0.4127 target = 0.150742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117441 restraints weight = 9113.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122123 restraints weight = 5998.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125539 restraints weight = 4405.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128029 restraints weight = 3487.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129810 restraints weight = 2891.070| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.7117 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= 0.101 Angle : 0.595 7.554 40103 Z= 0.296 Chirality : 0.042 0.138 4438 Planarity : 0.004 0.040 5187 Dihedral : 3.751 16.310 3941 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 are not related in a simple way. whole: 0.29 (0.15), residues: 3521 helix: 1.05 (0.14), residues: 1330 sheet: 0.61 (0.20), residues: 805 loop : -0.86 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 192 TYR 0.012 0.001 TYR G 602 PHE 0.022 0.001 PHE E 370 TRP 0.011 0.001 TRP D 392 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (29610) covalent geometry : angle 0.59471 / 0.30 (40103) hydrogen bonds : bond 0.03109 / 2.19 ( 1205) hydrogen bonds : angle 4.85147 / 3.39 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 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 118 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8646 (mp10) cc_final: 0.8406 (mp10) REVERT: B 79 ARG cc_start: 0.6951 (ptt180) cc_final: 0.6552 (ttp-110) REVERT: B 125 PHE cc_start: 0.8385 (t80) cc_final: 0.8016 (t80) REVERT: B 152 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6587 (mm-30) REVERT: B 184 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7284 (mmmt) REVERT: B 206 PHE cc_start: 0.8156 (m-80) cc_final: 0.7707 (m-80) REVERT: B 285 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7230 (mtt-85) REVERT: B 299 GLU cc_start: 0.7232 (tt0) cc_final: 0.6981 (tt0) REVERT: B 304 ILE cc_start: 0.7226 (mt) cc_final: 0.6946 (mp) REVERT: B 306 PHE cc_start: 0.7850 (m-80) cc_final: 0.7271 (m-80) REVERT: B 321 PHE cc_start: 0.8204 (m-10) cc_final: 0.7351 (m-10) REVERT: B 324 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8688 (mtmt) REVERT: B 331 PHE cc_start: 0.7487 (m-80) cc_final: 0.7199 (m-10) REVERT: B 332 LEU cc_start: 0.7527 (mt) cc_final: 0.7261 (mt) REVERT: B 360 LEU cc_start: 0.7613 (mt) cc_final: 0.7068 (mt) REVERT: B 370 PHE cc_start: 0.6483 (p90) cc_final: 0.6214 (p90) REVERT: B 383 ASN cc_start: 0.8255 (t0) cc_final: 0.8046 (t0) REVERT: B 425 ILE cc_start: 0.8650 (tp) cc_final: 0.8394 (tp) REVERT: B 437 VAL cc_start: 0.7186 (t) cc_final: 0.6935 (p) REVERT: B 441 TRP cc_start: 0.5446 (t-100) cc_final: 0.5117 (t-100) REVERT: B 455 MET cc_start: 0.8310 (mtp) cc_final: 0.8083 (mtp) REVERT: B 495 ARG cc_start: 0.8590 (tpt170) cc_final: 0.8171 (tpt90) REVERT: B 501 MET cc_start: 0.8282 (mtm) cc_final: 0.7868 (mtm) REVERT: B 509 ASP cc_start: 0.7544 (m-30) cc_final: 0.7179 (m-30) REVERT: B 510 ILE cc_start: 0.8538 (mm) cc_final: 0.8151 (mm) REVERT: B 522 MET cc_start: 0.7893 (mtt) cc_final: 0.7305 (mtt) REVERT: B 591 ASP cc_start: 0.5107 (m-30) cc_final: 0.4243 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0877 time to fit residues: 12.5314 Evaluate side-chains 104 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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: 1.9990 chunk 170 optimal weight: 3.9990 chunk 230 optimal weight: 0.0970 chunk 68 optimal weight: 0.0000 chunk 80 optimal weight: 0.5980 chunk 237 optimal weight: 0.0570 chunk 175 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 179 optimal weight: 0.2980 chunk 221 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 overall best weight: 0.0516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.153335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120948 restraints weight = 8748.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125597 restraints weight = 5772.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129022 restraints weight = 4223.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131410 restraints weight = 3313.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.133097 restraints weight = 2736.298| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.7292 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= 0.098 Angle : 0.585 7.658 40103 Z= 0.292 Chirality : 0.042 0.134 4438 Planarity : 0.004 0.034 5187 Dihedral : 3.768 16.506 3941 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 are not related in a simple way. whole: 0.40 (0.15), residues: 3521 helix: 1.02 (0.14), residues: 1344 sheet: 0.74 (0.20), residues: 798 loop : -0.71 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 192 TYR 0.012 0.001 TYR G 602 PHE 0.021 0.001 PHE A 370 TRP 0.032 0.002 TRP E 165 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (29610) covalent geometry : angle 0.58485 / 0.29 (40103) hydrogen bonds : bond 0.03039 / 2.15 ( 1205) hydrogen bonds : angle 4.78919 / 3.36 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 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 121 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 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 125 PHE cc_start: 0.8356 (t80) cc_final: 0.8017 (t80) REVERT: B 184 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7268 (mmmt) REVERT: B 206 PHE cc_start: 0.8055 (m-80) cc_final: 0.7611 (m-80) REVERT: B 248 PHE cc_start: 0.7508 (t80) cc_final: 0.7151 (t80) REVERT: B 285 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7226 (mtt180) REVERT: B 299 GLU cc_start: 0.7514 (tt0) cc_final: 0.6928 (tt0) REVERT: B 306 PHE cc_start: 0.7802 (m-80) cc_final: 0.7173 (m-80) REVERT: B 321 PHE cc_start: 0.8152 (m-10) cc_final: 0.7260 (m-10) REVERT: B 332 LEU cc_start: 0.7446 (mt) cc_final: 0.7238 (mt) REVERT: B 360 LEU cc_start: 0.7522 (mt) cc_final: 0.7128 (mt) REVERT: B 370 PHE cc_start: 0.6475 (p90) cc_final: 0.6191 (p90) REVERT: B 376 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 437 VAL cc_start: 0.7127 (t) cc_final: 0.6914 (p) REVERT: B 455 MET cc_start: 0.8399 (mtp) cc_final: 0.8162 (mtp) REVERT: B 470 LYS cc_start: 0.7934 (mttt) cc_final: 0.7672 (mmtt) REVERT: B 495 ARG cc_start: 0.8583 (tpt170) cc_final: 0.8117 (tpt90) REVERT: B 501 MET cc_start: 0.8293 (mtm) cc_final: 0.7903 (mtm) REVERT: B 509 ASP cc_start: 0.7552 (m-30) cc_final: 0.6821 (m-30) REVERT: B 510 ILE cc_start: 0.8534 (mm) cc_final: 0.8135 (tp) REVERT: B 522 MET cc_start: 0.7897 (mtt) cc_final: 0.7251 (mtt) REVERT: B 591 ASP cc_start: 0.5098 (m-30) cc_final: 0.4215 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0753 time to fit residues: 11.2741 Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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: 1.9990 chunk 352 optimal weight: 0.0050 chunk 296 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 192 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 328 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 overall best weight: 0.3292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 604 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 = 0.4102 r_free = 0.4102 target = 0.150506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118963 restraints weight = 9053.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.123498 restraints weight = 5878.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126799 restraints weight = 4286.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129175 restraints weight = 3365.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.130817 restraints weight = 2787.720| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.7683 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= 0.095 Angle : 0.573 7.624 40103 Z= 0.288 Chirality : 0.042 0.126 4438 Planarity : 0.004 0.037 5187 Dihedral : 3.729 15.245 3941 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 are not related in a simple way. whole: 0.44 (0.15), residues: 3521 helix: 1.12 (0.15), residues: 1344 sheet: 0.77 (0.20), residues: 798 loop : -0.76 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 192 TYR 0.013 0.001 TYR C 602 PHE 0.022 0.001 PHE A 370 TRP 0.032 0.002 TRP A 165 HIS 0.002 0.000 HIS G 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (29610) covalent geometry : angle 0.57344 / 0.29 (40103) hydrogen bonds : bond 0.03020 / 2.15 ( 1205) hydrogen bonds : angle 4.73312 / 3.31 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.41 seconds wall clock time: 40 minutes 14.33 seconds (2414.33 seconds total)