Starting phenix.real_space_refine on Wed Jun 25 04:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.map" model { file = "/net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8c_25744/06_2025/7t8c_25744.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F Time building chain proxies: 11.74, per 1000 atoms: 0.41 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: 6.80 Conformation dependent library (CDL) restraints added in 4.3 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: 4.30 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: 13.69 Time building geometry restraints manager: 7.92 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 61.670 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.025 29610 Z= 0.078 Angle : 0.416 4.822 40103 Z= 0.222 Chirality : 0.037 0.130 4438 Planarity : 0.003 0.024 5187 Dihedral : 7.595 83.072 10857 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.41 % Allowed : 2.71 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.003 0.001 TRP F 122 HIS 0.002 0.000 HIS E 552 PHE 0.004 0.001 PHE E 111 TYR 0.004 0.001 TYR B 602 ARG 0.001 0.000 ARG G 303 Details of bonding type rmsd hydrogen bonds : bond 0.23077 ( 1205) hydrogen bonds : angle 7.21589 ( 3300) covalent geometry : bond 0.00143 (29610) covalent geometry : angle 0.41560 (40103) *********************** 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 : 0.414 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: 0.7171 (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: 0.7416 (mp) REVERT: A 206 PHE cc_start: 0.7601 (m-80) cc_final: 0.7377 (m-80) REVERT: A 282 THR cc_start: 0.7186 (p) cc_final: 0.5671 (t) REVERT: A 299 GLU cc_start: 0.6479 (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: 0.7936 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 321 PHE cc_start: 0.7409 (m-10) cc_final: 0.6932 (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: 0.5361 (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: 0.2296 time to fit residues: 37.9465 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 : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 0.8980 chunk 270 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 279 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 0.0060 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 HIS ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.121336 restraints weight = 8883.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125808 restraints weight = 5677.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128879 restraints weight = 4066.316| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29610 Z= 0.102 Angle : 0.548 7.664 40103 Z= 0.280 Chirality : 0.041 0.128 4438 Planarity : 0.004 0.028 5187 Dihedral : 3.442 16.782 3941 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3521 helix: 1.40 (0.15), residues: 1302 sheet: 0.55 (0.19), residues: 833 loop : -0.37 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 363 HIS 0.004 0.001 HIS D 552 PHE 0.015 0.001 PHE G 520 TYR 0.011 0.001 TYR B 537 ARG 0.004 0.000 ARG G 202 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1205) hydrogen bonds : angle 5.36991 ( 3300) covalent geometry : bond 0.00221 (29610) covalent geometry : angle 0.54801 (40103) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8973 (ptp90) cc_final: 0.8721 (ptp90) REVERT: B 69 ILE cc_start: 0.8263 (mp) cc_final: 0.7831 (tp) REVERT: B 79 ARG cc_start: 0.6876 (ptt180) cc_final: 0.6551 (ptt-90) REVERT: B 104 ILE cc_start: 0.8205 (mm) cc_final: 0.7827 (tp) REVERT: B 125 PHE cc_start: 0.8268 (t80) cc_final: 0.7994 (t80) REVERT: B 186 THR cc_start: 0.6534 (p) cc_final: 0.5657 (t) REVERT: B 206 PHE cc_start: 0.8378 (m-80) cc_final: 0.8118 (m-80) REVERT: B 283 LEU cc_start: 0.8228 (mt) cc_final: 0.7915 (mt) REVERT: B 285 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7255 (mtt180) REVERT: B 295 LEU cc_start: 0.8398 (mt) cc_final: 0.8137 (mt) REVERT: B 299 GLU cc_start: 0.7356 (tt0) cc_final: 0.6557 (tt0) REVERT: B 304 ILE cc_start: 0.7335 (mt) cc_final: 0.7044 (mp) REVERT: B 316 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 321 PHE cc_start: 0.8032 (m-10) cc_final: 0.7394 (m-10) REVERT: B 357 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6973 (mtm110) REVERT: B 423 THR cc_start: 0.6667 (p) cc_final: 0.6392 (t) REVERT: B 451 LEU cc_start: 0.7937 (tp) cc_final: 0.7552 (tp) REVERT: B 455 MET cc_start: 0.7923 (mtp) cc_final: 0.7414 (mtp) REVERT: B 492 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6996 (tp-100) REVERT: B 501 MET cc_start: 0.7981 (mtp) cc_final: 0.7718 (mtp) REVERT: B 509 ASP cc_start: 0.7709 (m-30) cc_final: 0.7175 (m-30) REVERT: B 510 ILE cc_start: 0.8215 (mm) cc_final: 0.7706 (tp) REVERT: B 512 HIS cc_start: 0.7349 (t-170) cc_final: 0.7118 (t70) REVERT: B 520 PHE cc_start: 0.7746 (t80) cc_final: 0.7253 (t80) REVERT: B 543 ARG cc_start: 0.6907 (tpt170) cc_final: 0.5616 (mmm160) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2141 time to fit residues: 33.8052 Evaluate side-chains 111 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 18 optimal weight: 0.9980 chunk 323 optimal weight: 0.0010 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 354 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.149252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.118235 restraints weight = 8834.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122886 restraints weight = 5721.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126117 restraints weight = 4130.118| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4469 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= 0.103 Angle : 0.543 6.703 40103 Z= 0.280 Chirality : 0.042 0.130 4438 Planarity : 0.004 0.030 5187 Dihedral : 3.779 19.740 3941 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3521 helix: 1.19 (0.15), residues: 1309 sheet: 0.48 (0.20), residues: 833 loop : -0.45 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 363 HIS 0.002 0.001 HIS G 75 PHE 0.022 0.001 PHE D 478 TYR 0.011 0.001 TYR C 602 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1205) hydrogen bonds : angle 5.23344 ( 3300) covalent geometry : bond 0.00218 (29610) covalent geometry : angle 0.54332 (40103) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8314 (mp) cc_final: 0.8044 (mm) REVERT: B 105 ASP cc_start: 0.7495 (t0) cc_final: 0.7062 (t0) REVERT: B 125 PHE cc_start: 0.8391 (t80) cc_final: 0.8035 (t80) REVERT: B 152 GLU cc_start: 0.5932 (mm-30) cc_final: 0.5729 (mm-30) REVERT: B 206 PHE cc_start: 0.8352 (m-80) cc_final: 0.8094 (m-80) REVERT: B 285 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7314 (mtt180) REVERT: B 295 LEU cc_start: 0.8556 (mt) cc_final: 0.8281 (mt) REVERT: B 299 GLU cc_start: 0.7016 (tt0) cc_final: 0.6210 (tt0) REVERT: B 304 ILE cc_start: 0.7279 (mt) cc_final: 0.6986 (mp) REVERT: B 316 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 321 PHE cc_start: 0.8286 (m-10) cc_final: 0.7659 (m-10) REVERT: B 324 LYS cc_start: 0.8829 (mttt) cc_final: 0.8579 (mttt) REVERT: B 350 PHE cc_start: 0.7197 (t80) cc_final: 0.6880 (t80) REVERT: B 355 ILE cc_start: 0.8482 (mt) cc_final: 0.8218 (mt) REVERT: B 357 ARG cc_start: 0.7380 (mtm110) cc_final: 0.7020 (mtm110) REVERT: B 360 LEU cc_start: 0.7161 (mt) cc_final: 0.6935 (mt) REVERT: B 423 THR cc_start: 0.6780 (p) cc_final: 0.6522 (t) REVERT: B 437 VAL cc_start: 0.6632 (t) cc_final: 0.6312 (p) REVERT: B 451 LEU cc_start: 0.8091 (tp) cc_final: 0.7721 (tp) REVERT: B 453 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8224 (mtp85) REVERT: B 455 MET cc_start: 0.7980 (mtp) cc_final: 0.7570 (mtp) REVERT: B 496 THR cc_start: 0.8628 (m) cc_final: 0.8313 (p) REVERT: B 501 MET cc_start: 0.7963 (mtp) cc_final: 0.7665 (mtp) REVERT: B 509 ASP cc_start: 0.7712 (m-30) cc_final: 0.6916 (m-30) REVERT: B 510 ILE cc_start: 0.8472 (mm) cc_final: 0.7983 (tp) REVERT: B 543 ARG cc_start: 0.7291 (tpt170) cc_final: 0.6586 (tpt170) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2501 time to fit residues: 38.9711 Evaluate side-chains 114 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 231 optimal weight: 0.0670 chunk 312 optimal weight: 0.0980 chunk 165 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 217 optimal weight: 0.0770 chunk 343 optimal weight: 0.2980 chunk 328 optimal weight: 0.4980 chunk 352 optimal weight: 0.1980 chunk 332 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 342 optimal weight: 0.9980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.152813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121880 restraints weight = 8921.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.126515 restraints weight = 5764.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129910 restraints weight = 4154.003| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.4774 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= 0.092 Angle : 0.514 6.669 40103 Z= 0.260 Chirality : 0.041 0.132 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.625 19.841 3941 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3521 helix: 1.00 (0.15), residues: 1309 sheet: 0.40 (0.20), residues: 833 loop : -0.53 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 165 HIS 0.002 0.000 HIS E 512 PHE 0.022 0.001 PHE D 478 TYR 0.009 0.001 TYR G 484 ARG 0.002 0.000 ARG C 495 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 1205) hydrogen bonds : angle 5.06777 ( 3300) covalent geometry : bond 0.00198 (29610) covalent geometry : angle 0.51407 (40103) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8776 (mp10) cc_final: 0.8539 (mm110) REVERT: B 79 ARG cc_start: 0.7029 (ptt180) cc_final: 0.6703 (ttp-110) REVERT: B 105 ASP cc_start: 0.7679 (t0) cc_final: 0.7120 (t0) REVERT: B 125 PHE cc_start: 0.8359 (t80) cc_final: 0.8035 (t80) REVERT: B 206 PHE cc_start: 0.8348 (m-80) cc_final: 0.8141 (m-80) REVERT: B 285 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7310 (mtt180) REVERT: B 295 LEU cc_start: 0.8552 (mt) cc_final: 0.8288 (mt) REVERT: B 299 GLU cc_start: 0.7101 (tt0) cc_final: 0.6262 (tt0) REVERT: B 304 ILE cc_start: 0.7156 (mt) cc_final: 0.6912 (mp) REVERT: B 313 ARG cc_start: 0.8458 (tmm-80) cc_final: 0.7830 (ptm160) REVERT: B 316 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 321 PHE cc_start: 0.8227 (m-10) cc_final: 0.7621 (m-10) REVERT: B 324 LYS cc_start: 0.8803 (mttt) cc_final: 0.8501 (mttt) REVERT: B 350 PHE cc_start: 0.7091 (t80) cc_final: 0.6726 (t80) REVERT: B 355 ILE cc_start: 0.8400 (mt) cc_final: 0.8020 (mt) REVERT: B 357 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7104 (mtm110) REVERT: B 392 TRP cc_start: 0.6260 (m-90) cc_final: 0.6035 (m-90) REVERT: B 437 VAL cc_start: 0.6624 (t) cc_final: 0.6348 (p) REVERT: B 451 LEU cc_start: 0.8050 (tp) cc_final: 0.7727 (tp) REVERT: B 455 MET cc_start: 0.7914 (mtp) cc_final: 0.7505 (mtp) REVERT: B 496 THR cc_start: 0.8691 (m) cc_final: 0.8432 (p) REVERT: B 509 ASP cc_start: 0.7638 (m-30) cc_final: 0.6792 (m-30) REVERT: B 510 ILE cc_start: 0.8434 (mm) cc_final: 0.8012 (tp) REVERT: B 582 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6039 (mm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2247 time to fit residues: 30.4794 Evaluate side-chains 102 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 111 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 239 optimal weight: 0.0570 chunk 187 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 207 optimal weight: 0.4980 chunk 310 optimal weight: 0.3980 chunk 290 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 347 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.119315 restraints weight = 9141.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.124091 restraints weight = 5893.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.127575 restraints weight = 4216.997| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.5373 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 : 0.533 6.683 40103 Z= 0.270 Chirality : 0.041 0.150 4438 Planarity : 0.003 0.031 5187 Dihedral : 3.569 19.098 3941 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3521 helix: 1.08 (0.15), residues: 1309 sheet: 0.59 (0.21), residues: 798 loop : -0.65 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 165 HIS 0.002 0.000 HIS G 405 PHE 0.018 0.001 PHE E 478 TYR 0.011 0.001 TYR C 602 ARG 0.004 0.000 ARG C 453 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 1205) hydrogen bonds : angle 5.09396 ( 3300) covalent geometry : bond 0.00203 (29610) covalent geometry : angle 0.53251 (40103) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8803 (mp10) cc_final: 0.8544 (mm110) REVERT: B 79 ARG cc_start: 0.6962 (ptt180) cc_final: 0.6558 (ptt-90) REVERT: B 105 ASP cc_start: 0.7727 (t0) cc_final: 0.7119 (t0) REVERT: B 125 PHE cc_start: 0.8389 (t80) cc_final: 0.8062 (t80) REVERT: B 206 PHE cc_start: 0.8281 (m-80) cc_final: 0.8018 (m-80) REVERT: B 248 PHE cc_start: 0.7588 (t80) cc_final: 0.5634 (t80) REVERT: B 285 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7190 (mtt180) REVERT: B 287 THR cc_start: 0.8137 (p) cc_final: 0.7909 (p) REVERT: B 299 GLU cc_start: 0.7068 (tt0) cc_final: 0.6270 (tt0) REVERT: B 304 ILE cc_start: 0.7146 (mt) cc_final: 0.6886 (mp) REVERT: B 321 PHE cc_start: 0.8322 (m-10) cc_final: 0.7559 (m-10) REVERT: B 355 ILE cc_start: 0.8451 (mt) cc_final: 0.8119 (mt) REVERT: B 357 ARG cc_start: 0.7344 (mtm110) cc_final: 0.7042 (mtm110) REVERT: B 425 ILE cc_start: 0.8416 (tp) cc_final: 0.8181 (tp) REVERT: B 437 VAL cc_start: 0.6744 (t) cc_final: 0.6446 (p) REVERT: B 447 SER cc_start: 0.6453 (t) cc_final: 0.6237 (t) REVERT: B 455 MET cc_start: 0.7947 (mtp) cc_final: 0.7614 (mtp) REVERT: B 496 THR cc_start: 0.8650 (m) cc_final: 0.8434 (p) REVERT: B 500 THR cc_start: 0.8475 (m) cc_final: 0.8239 (p) REVERT: B 509 ASP cc_start: 0.7634 (m-30) cc_final: 0.6890 (m-30) REVERT: B 510 ILE cc_start: 0.8538 (mm) cc_final: 0.8113 (tp) REVERT: B 539 ILE cc_start: 0.8179 (mt) cc_final: 0.7947 (mt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1782 time to fit residues: 24.3808 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 329 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 190 optimal weight: 0.0070 chunk 338 optimal weight: 0.1980 chunk 141 optimal weight: 0.8980 chunk 207 optimal weight: 0.0000 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118355 restraints weight = 8946.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122857 restraints weight = 5920.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126175 restraints weight = 4350.240| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29610 Z= 0.097 Angle : 0.528 7.520 40103 Z= 0.268 Chirality : 0.041 0.139 4438 Planarity : 0.003 0.033 5187 Dihedral : 3.613 18.149 3941 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3521 helix: 1.15 (0.15), residues: 1288 sheet: 0.52 (0.21), residues: 798 loop : -0.66 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 441 HIS 0.002 0.001 HIS G 512 PHE 0.015 0.001 PHE B 478 TYR 0.012 0.001 TYR E 428 ARG 0.004 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 1205) hydrogen bonds : angle 4.97881 ( 3300) covalent geometry : bond 0.00212 (29610) covalent geometry : angle 0.52808 (40103) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 79 ARG cc_start: 0.6986 (ptt180) cc_final: 0.6567 (ptt-90) REVERT: B 105 ASP cc_start: 0.7714 (t0) cc_final: 0.7108 (t0) REVERT: B 125 PHE cc_start: 0.8424 (t80) cc_final: 0.8093 (t80) REVERT: B 283 LEU cc_start: 0.8149 (mt) cc_final: 0.7894 (mp) REVERT: B 285 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7262 (mtt180) REVERT: B 287 THR cc_start: 0.8249 (p) cc_final: 0.8045 (p) REVERT: B 299 GLU cc_start: 0.7044 (tt0) cc_final: 0.6221 (tt0) REVERT: B 304 ILE cc_start: 0.7173 (mt) cc_final: 0.6960 (mp) REVERT: B 321 PHE cc_start: 0.8240 (m-10) cc_final: 0.7514 (m-10) REVERT: B 355 ILE cc_start: 0.8559 (mt) cc_final: 0.8229 (mt) REVERT: B 356 LEU cc_start: 0.8615 (pp) cc_final: 0.8408 (pp) REVERT: B 357 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6998 (mtm110) REVERT: B 425 ILE cc_start: 0.8512 (tp) cc_final: 0.8241 (tp) REVERT: B 437 VAL cc_start: 0.6891 (t) cc_final: 0.6574 (p) REVERT: B 447 SER cc_start: 0.6576 (t) cc_final: 0.6363 (t) REVERT: B 470 LYS cc_start: 0.8068 (mttt) cc_final: 0.7830 (mmtt) REVERT: B 483 LEU cc_start: 0.7719 (tp) cc_final: 0.7467 (tp) REVERT: B 496 THR cc_start: 0.8628 (m) cc_final: 0.8424 (p) REVERT: B 500 THR cc_start: 0.8538 (m) cc_final: 0.8330 (p) REVERT: B 501 MET cc_start: 0.8134 (mtm) cc_final: 0.7847 (mtm) REVERT: B 509 ASP cc_start: 0.6979 (m-30) cc_final: 0.6424 (m-30) REVERT: B 510 ILE cc_start: 0.8437 (mm) cc_final: 0.8020 (tp) REVERT: B 582 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6310 (mm-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1976 time to fit residues: 25.7882 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 284 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 322 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 334 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 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 = 0.4118 r_free = 0.4118 target = 0.148785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116761 restraints weight = 8974.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121110 restraints weight = 5969.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.124308 restraints weight = 4407.557| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29610 Z= 0.111 Angle : 0.574 7.498 40103 Z= 0.293 Chirality : 0.042 0.137 4438 Planarity : 0.003 0.032 5187 Dihedral : 3.629 17.802 3941 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3521 helix: 1.13 (0.15), residues: 1344 sheet: 0.50 (0.21), residues: 798 loop : -0.76 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 441 HIS 0.002 0.001 HIS G 512 PHE 0.015 0.001 PHE C 248 TYR 0.011 0.001 TYR C 602 ARG 0.006 0.000 ARG G 192 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 1205) hydrogen bonds : angle 5.00473 ( 3300) covalent geometry : bond 0.00235 (29610) covalent geometry : angle 0.57419 (40103) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.7017 (ptt180) cc_final: 0.6613 (ptt-90) REVERT: B 105 ASP cc_start: 0.7709 (t0) cc_final: 0.7090 (t0) REVERT: B 125 PHE cc_start: 0.8426 (t80) cc_final: 0.8090 (t80) REVERT: B 206 PHE cc_start: 0.7817 (m-80) cc_final: 0.7553 (m-80) REVERT: B 283 LEU cc_start: 0.8108 (mt) cc_final: 0.7817 (mp) REVERT: B 285 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7183 (mtt180) REVERT: B 299 GLU cc_start: 0.7145 (tt0) cc_final: 0.6363 (tt0) REVERT: B 321 PHE cc_start: 0.8319 (m-10) cc_final: 0.7551 (m-10) REVERT: B 323 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8109 (tpp80) REVERT: B 324 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8579 (mtmt) REVERT: B 355 ILE cc_start: 0.8625 (mt) cc_final: 0.8356 (mt) REVERT: B 357 ARG cc_start: 0.7364 (mtm110) cc_final: 0.6928 (mtm180) REVERT: B 360 LEU cc_start: 0.7592 (mt) cc_final: 0.7299 (mt) REVERT: B 437 VAL cc_start: 0.7022 (t) cc_final: 0.6742 (p) REVERT: B 470 LYS cc_start: 0.8057 (mttt) cc_final: 0.7823 (mmtt) REVERT: B 495 ARG cc_start: 0.8638 (tpt170) cc_final: 0.8398 (tpt90) REVERT: B 496 THR cc_start: 0.8663 (m) cc_final: 0.8418 (p) REVERT: B 501 MET cc_start: 0.8270 (mtm) cc_final: 0.8001 (mtm) REVERT: B 509 ASP cc_start: 0.7525 (m-30) cc_final: 0.6991 (m-30) REVERT: B 510 ILE cc_start: 0.8555 (mm) cc_final: 0.8258 (tp) REVERT: B 522 MET cc_start: 0.8228 (mtm) cc_final: 0.7955 (mtm) REVERT: B 539 ILE cc_start: 0.8312 (mt) cc_final: 0.8076 (mt) REVERT: B 582 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6453 (mm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2963 time to fit residues: 41.8264 Evaluate side-chains 103 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 30 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 341 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 308 optimal weight: 0.0170 chunk 282 optimal weight: 0.5980 chunk 200 optimal weight: 0.0170 chunk 160 optimal weight: 0.5980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 492 GLN ** B 512 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.150838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117732 restraints weight = 9064.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122391 restraints weight = 6022.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125823 restraints weight = 4441.827| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29610 Z= 0.098 Angle : 0.549 5.811 40103 Z= 0.278 Chirality : 0.042 0.130 4438 Planarity : 0.003 0.032 5187 Dihedral : 3.526 16.735 3941 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3521 helix: 1.07 (0.15), residues: 1302 sheet: 0.52 (0.21), residues: 798 loop : -0.57 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.001 0.000 HIS B 512 PHE 0.026 0.001 PHE G 248 TYR 0.014 0.001 TYR G 428 ARG 0.004 0.000 ARG C 192 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 1205) hydrogen bonds : angle 4.97719 ( 3300) covalent geometry : bond 0.00214 (29610) covalent geometry : angle 0.54928 (40103) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.8660 (mp10) cc_final: 0.8445 (mm-40) REVERT: B 79 ARG cc_start: 0.7054 (ptt180) cc_final: 0.6701 (ptt-90) REVERT: B 105 ASP cc_start: 0.7640 (t0) cc_final: 0.6857 (t0) REVERT: B 125 PHE cc_start: 0.8439 (t80) cc_final: 0.8093 (t80) REVERT: B 206 PHE cc_start: 0.7968 (m-80) cc_final: 0.7602 (m-80) REVERT: B 266 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 283 LEU cc_start: 0.7984 (mt) cc_final: 0.7701 (mp) REVERT: B 285 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7157 (mtt180) REVERT: B 299 GLU cc_start: 0.7213 (tt0) cc_final: 0.6700 (tt0) REVERT: B 302 ARG cc_start: 0.7572 (ppt170) cc_final: 0.7321 (ppt170) REVERT: B 304 ILE cc_start: 0.7112 (mt) cc_final: 0.6805 (mp) REVERT: B 321 PHE cc_start: 0.8340 (m-10) cc_final: 0.7662 (m-10) REVERT: B 323 ARG cc_start: 0.8504 (tpp80) cc_final: 0.7923 (tpp80) REVERT: B 360 LEU cc_start: 0.7599 (mt) cc_final: 0.7276 (mt) REVERT: B 383 ASN cc_start: 0.8308 (t0) cc_final: 0.8083 (t0) REVERT: B 437 VAL cc_start: 0.7004 (t) cc_final: 0.6710 (p) REVERT: B 455 MET cc_start: 0.8258 (mtt) cc_final: 0.7952 (mtt) REVERT: B 470 LYS cc_start: 0.7956 (mttt) cc_final: 0.7723 (mmtt) REVERT: B 496 THR cc_start: 0.8652 (m) cc_final: 0.8339 (p) REVERT: B 501 MET cc_start: 0.8232 (mtm) cc_final: 0.7786 (mtm) REVERT: B 509 ASP cc_start: 0.7503 (m-30) cc_final: 0.6903 (m-30) REVERT: B 510 ILE cc_start: 0.8440 (mm) cc_final: 0.8150 (tp) REVERT: B 522 MET cc_start: 0.8194 (mtm) cc_final: 0.7973 (mtm) REVERT: B 535 GLN cc_start: 0.5670 (tm-30) cc_final: 0.5410 (tm-30) REVERT: B 539 ILE cc_start: 0.8067 (mt) cc_final: 0.7802 (mt) REVERT: B 582 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6353 (mm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2196 time to fit residues: 30.9537 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 : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 240 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 267 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 0.0370 chunk 350 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 183 optimal weight: 0.0070 chunk 330 optimal weight: 0.0980 chunk 173 optimal weight: 0.0000 overall best weight: 0.0478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.153835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121117 restraints weight = 8900.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125790 restraints weight = 5876.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129160 restraints weight = 4309.411| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 29610 Z= 0.096 Angle : 0.543 6.767 40103 Z= 0.272 Chirality : 0.042 0.127 4438 Planarity : 0.004 0.034 5187 Dihedral : 3.506 16.357 3941 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3521 helix: 1.04 (0.15), residues: 1302 sheet: 0.55 (0.21), residues: 798 loop : -0.56 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 158 HIS 0.003 0.001 HIS G 512 PHE 0.020 0.001 PHE G 488 TYR 0.011 0.001 TYR D 602 ARG 0.004 0.000 ARG G 329 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 1205) hydrogen bonds : angle 4.90649 ( 3300) covalent geometry : bond 0.00207 (29610) covalent geometry : angle 0.54318 (40103) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.9092 (ptp-170) cc_final: 0.8782 (ptp-110) REVERT: B 62 GLN cc_start: 0.8736 (mp10) cc_final: 0.8506 (mm-40) REVERT: B 79 ARG cc_start: 0.6991 (ptt180) cc_final: 0.6691 (ptt-90) REVERT: B 125 PHE cc_start: 0.8455 (t80) cc_final: 0.8107 (t80) REVERT: B 206 PHE cc_start: 0.8047 (m-80) cc_final: 0.7687 (m-80) REVERT: B 283 LEU cc_start: 0.7886 (mt) cc_final: 0.7606 (mp) REVERT: B 285 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.6861 (mmm-85) REVERT: B 295 LEU cc_start: 0.8842 (mt) cc_final: 0.8635 (mt) REVERT: B 299 GLU cc_start: 0.7330 (tt0) cc_final: 0.6458 (tt0) REVERT: B 304 ILE cc_start: 0.7020 (mt) cc_final: 0.6735 (mp) REVERT: B 321 PHE cc_start: 0.8352 (m-10) cc_final: 0.7557 (m-10) REVERT: B 324 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8693 (mtmt) REVERT: B 360 LEU cc_start: 0.7500 (mt) cc_final: 0.7230 (mt) REVERT: B 383 ASN cc_start: 0.8268 (t0) cc_final: 0.8040 (t0) REVERT: B 437 VAL cc_start: 0.6852 (t) cc_final: 0.6603 (p) REVERT: B 455 MET cc_start: 0.8287 (mtt) cc_final: 0.8027 (mtt) REVERT: B 470 LYS cc_start: 0.7930 (mttt) cc_final: 0.7693 (mmtt) REVERT: B 496 THR cc_start: 0.8588 (m) cc_final: 0.8296 (p) REVERT: B 501 MET cc_start: 0.8197 (mtm) cc_final: 0.7859 (mtm) REVERT: B 509 ASP cc_start: 0.7520 (m-30) cc_final: 0.7046 (m-30) REVERT: B 510 ILE cc_start: 0.8495 (mm) cc_final: 0.8079 (tp) REVERT: B 522 MET cc_start: 0.8085 (mtm) cc_final: 0.7832 (mtm) REVERT: B 539 ILE cc_start: 0.7988 (mt) cc_final: 0.7753 (mt) REVERT: B 582 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6359 (mm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2546 time to fit residues: 35.9114 Evaluate side-chains 99 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 238 optimal weight: 0.0070 chunk 219 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 128 optimal weight: 0.0170 chunk 220 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 327 optimal weight: 0.0770 chunk 185 optimal weight: 3.9990 chunk 283 optimal weight: 0.0040 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121527 restraints weight = 8923.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126007 restraints weight = 5922.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129319 restraints weight = 4351.844| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.6890 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= 0.100 Angle : 0.578 9.277 40103 Z= 0.294 Chirality : 0.043 0.150 4438 Planarity : 0.004 0.034 5187 Dihedral : 3.609 17.708 3941 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3521 helix: 0.95 (0.15), residues: 1309 sheet: 0.51 (0.20), residues: 798 loop : -0.50 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.002 0.000 HIS G 512 PHE 0.033 0.001 PHE F 478 TYR 0.016 0.001 TYR G 602 ARG 0.007 0.000 ARG D 495 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1205) hydrogen bonds : angle 4.90512 ( 3300) covalent geometry : bond 0.00218 (29610) covalent geometry : angle 0.57776 (40103) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.9080 (ptp-170) cc_final: 0.8861 (ptp-110) REVERT: B 125 PHE cc_start: 0.8429 (t80) cc_final: 0.8077 (t80) REVERT: B 172 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7056 (mp0) REVERT: B 206 PHE cc_start: 0.7938 (m-80) cc_final: 0.7569 (m-80) REVERT: B 285 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.6843 (mmm-85) REVERT: B 299 GLU cc_start: 0.7321 (tt0) cc_final: 0.6447 (tt0) REVERT: B 304 ILE cc_start: 0.7036 (mt) cc_final: 0.6742 (mp) REVERT: B 321 PHE cc_start: 0.8360 (m-10) cc_final: 0.7650 (m-10) REVERT: B 360 LEU cc_start: 0.7505 (mt) cc_final: 0.7200 (mt) REVERT: B 437 VAL cc_start: 0.6894 (t) cc_final: 0.6640 (p) REVERT: B 455 MET cc_start: 0.8243 (mtt) cc_final: 0.7986 (mtt) REVERT: B 496 THR cc_start: 0.8527 (m) cc_final: 0.8248 (p) REVERT: B 497 VAL cc_start: 0.8804 (m) cc_final: 0.8257 (m) REVERT: B 501 MET cc_start: 0.8201 (mtm) cc_final: 0.7912 (mtm) REVERT: B 509 ASP cc_start: 0.7551 (m-30) cc_final: 0.6954 (m-30) REVERT: B 510 ILE cc_start: 0.8496 (mm) cc_final: 0.8091 (tp) REVERT: B 535 GLN cc_start: 0.5713 (tm-30) cc_final: 0.5318 (pp30) REVERT: B 539 ILE cc_start: 0.7922 (mt) cc_final: 0.7701 (mt) REVERT: B 582 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6373 (mm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1878 time to fit residues: 26.2602 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 : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 184 optimal weight: 0.0870 chunk 309 optimal weight: 3.9990 chunk 20 optimal weight: 0.0010 chunk 191 optimal weight: 0.9980 chunk 214 optimal weight: 0.0370 chunk 140 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 157 optimal weight: 0.0010 chunk 152 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 150 optimal weight: 0.0970 overall best weight: 0.0446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4196 r_free = 0.4196 target = 0.155678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122376 restraints weight = 9136.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127019 restraints weight = 6102.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.130445 restraints weight = 4534.996| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 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 0.030 29610 Z= 0.100 Angle : 0.568 7.646 40103 Z= 0.287 Chirality : 0.043 0.159 4438 Planarity : 0.004 0.060 5187 Dihedral : 3.495 13.300 3941 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3521 helix: 0.92 (0.14), residues: 1309 sheet: 0.67 (0.20), residues: 791 loop : -0.62 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 158 HIS 0.002 0.000 HIS G 512 PHE 0.013 0.001 PHE C 301 TYR 0.013 0.001 TYR F 602 ARG 0.012 0.000 ARG G 495 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 1205) hydrogen bonds : angle 4.88634 ( 3300) covalent geometry : bond 0.00221 (29610) covalent geometry : angle 0.56759 (40103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.65 seconds wall clock time: 86 minutes 56.09 seconds (5216.09 seconds total)