Starting phenix.real_space_refine on Mon May 26 11:51:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzw_42845/05_2025/8uzw_42845.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 140 5.16 5 C 17742 2.51 5 N 5071 2.21 5 O 5295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28258 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2894 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2902 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2884 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2921 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2779 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2774 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2881 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2737 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2738 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 18.17, per 1000 atoms: 0.64 Number of scatterers: 28258 At special positions: 0 Unit cell: (189.98, 183.372, 81.774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 10 15.00 O 5295 8.00 N 5071 7.00 C 17742 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.8 seconds 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6902 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 46 sheets defined 47.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.992A pdb=" N GLY A 96 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.682A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.696A pdb=" N ARG A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 4.344A pdb=" N ALA A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.520A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 6.540A pdb=" N GLU A 345 " --> pdb=" O LEU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 360 through 380 removed outlier: 3.953A pdb=" N ALA A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.967A pdb=" N LEU A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.553A pdb=" N LEU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.016A pdb=" N GLY B 96 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.677A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 319 through 325 removed outlier: 4.300A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 removed outlier: 3.525A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 341 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 4.274A pdb=" N SER B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 360 through 380 removed outlier: 3.533A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.121A pdb=" N LEU B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.824A pdb=" N GLY C 96 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 152 through 165 Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.525A pdb=" N TYR C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 215 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 319 through 325 removed outlier: 4.319A pdb=" N ALA C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 3.569A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 345 removed outlier: 6.570A pdb=" N GLU C 345 " --> pdb=" O LEU C 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 342 through 345' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 360 through 380 removed outlier: 3.724A pdb=" N ALA C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 417 through 430 removed outlier: 4.201A pdb=" N LEU C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 463 removed outlier: 3.610A pdb=" N LYS C 463 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.706A pdb=" N GLY D 96 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 152 through 165 Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.693A pdb=" N ALA D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 277 through 285 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 318 through 325 removed outlier: 4.306A pdb=" N ARG D 322 " --> pdb=" O HIS D 318 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 removed outlier: 3.737A pdb=" N TYR D 341 " --> pdb=" O THR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 4.185A pdb=" N SER D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 360 through 380 removed outlier: 4.068A pdb=" N ALA D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Proline residue: D 374 - end of helix Processing helix chain 'D' and resid 417 through 430 removed outlier: 4.114A pdb=" N LEU D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.934A pdb=" N PHE D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.880A pdb=" N GLY E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 114 Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 152 through 165 Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.534A pdb=" N TYR E 211 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 277 through 285 Processing helix chain 'E' and resid 308 through 317 Processing helix chain 'E' and resid 319 through 325 removed outlier: 4.391A pdb=" N ALA E 323 " --> pdb=" O PRO E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 3.742A pdb=" N TYR E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 345 removed outlier: 6.631A pdb=" N GLU E 345 " --> pdb=" O LEU E 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 345' Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 360 through 378 removed outlier: 3.690A pdb=" N ALA E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) Proline residue: E 374 - end of helix Processing helix chain 'E' and resid 423 through 430 removed outlier: 3.561A pdb=" N GLU E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 459 removed outlier: 3.728A pdb=" N PHE E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.925A pdb=" N GLY F 96 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 131 through 142 Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 186 through 193 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.545A pdb=" N TYR F 211 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 Processing helix chain 'F' and resid 266 through 271 Processing helix chain 'F' and resid 277 through 285 Processing helix chain 'F' and resid 308 through 317 Processing helix chain 'F' and resid 319 through 325 removed outlier: 4.351A pdb=" N ALA F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 removed outlier: 3.716A pdb=" N TYR F 341 " --> pdb=" O THR F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 345 removed outlier: 6.516A pdb=" N GLU F 345 " --> pdb=" O LEU F 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 342 through 345' Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.983A pdb=" N ALA F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 430 removed outlier: 3.629A pdb=" N GLU F 430 " --> pdb=" O ALA F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 462 removed outlier: 3.689A pdb=" N PHE F 457 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.911A pdb=" N GLY G 96 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 114 Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 152 through 165 Processing helix chain 'G' and resid 186 through 193 Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.693A pdb=" N ALA G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 252 Processing helix chain 'G' and resid 266 through 271 Processing helix chain 'G' and resid 277 through 285 Processing helix chain 'G' and resid 308 through 317 Processing helix chain 'G' and resid 319 through 325 removed outlier: 4.318A pdb=" N ALA G 323 " --> pdb=" O PRO G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 339 Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 346 through 351 Processing helix chain 'G' and resid 351 through 358 Processing helix chain 'G' and resid 360 through 380 removed outlier: 3.573A pdb=" N ILE G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA G 373 " --> pdb=" O GLN G 369 " (cutoff:3.500A) Proline residue: G 374 - end of helix Processing helix chain 'G' and resid 417 through 430 removed outlier: 4.109A pdb=" N LEU G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 451 No H-bonds generated for 'chain 'G' and resid 449 through 451' Processing helix chain 'G' and resid 453 through 462 removed outlier: 4.115A pdb=" N PHE G 457 " --> pdb=" O ASP G 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 96 removed outlier: 4.044A pdb=" N GLY H 96 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 114 Processing helix chain 'H' and resid 131 through 142 Processing helix chain 'H' and resid 152 through 165 Processing helix chain 'H' and resid 186 through 193 Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.668A pdb=" N ALA H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 215 " --> pdb=" O TYR H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 252 Processing helix chain 'H' and resid 266 through 271 Processing helix chain 'H' and resid 277 through 285 Processing helix chain 'H' and resid 308 through 317 Processing helix chain 'H' and resid 319 through 325 removed outlier: 4.339A pdb=" N ALA H 323 " --> pdb=" O PRO H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 3.781A pdb=" N TYR H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 345 removed outlier: 6.586A pdb=" N GLU H 345 " --> pdb=" O LEU H 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 342 through 345' Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 351 through 358 Processing helix chain 'H' and resid 360 through 371 Processing helix chain 'H' and resid 422 through 429 Processing helix chain 'H' and resid 453 through 461 removed outlier: 3.929A pdb=" N GLU H 459 " --> pdb=" O GLN H 455 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET H 460 " --> pdb=" O ARG H 456 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 461 " --> pdb=" O PHE H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 removed outlier: 4.058A pdb=" N GLY I 96 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 152 through 165 Processing helix chain 'I' and resid 186 through 193 Processing helix chain 'I' and resid 207 through 215 removed outlier: 3.535A pdb=" N TYR I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA I 214 " --> pdb=" O ASP I 210 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL I 215 " --> pdb=" O TYR I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 252 Processing helix chain 'I' and resid 266 through 271 Processing helix chain 'I' and resid 277 through 285 Processing helix chain 'I' and resid 308 through 317 Processing helix chain 'I' and resid 318 through 325 removed outlier: 4.402A pdb=" N ARG I 322 " --> pdb=" O HIS I 318 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA I 323 " --> pdb=" O PRO I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 339 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 343 through 351 removed outlier: 4.241A pdb=" N SER I 348 " --> pdb=" O PRO I 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU I 349 " --> pdb=" O GLU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 358 Processing helix chain 'I' and resid 360 through 371 Processing helix chain 'I' and resid 422 through 430 Processing helix chain 'I' and resid 453 through 462 Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.978A pdb=" N GLY J 96 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 114 Processing helix chain 'J' and resid 131 through 142 Processing helix chain 'J' and resid 152 through 165 Processing helix chain 'J' and resid 186 through 193 Processing helix chain 'J' and resid 207 through 215 removed outlier: 3.664A pdb=" N ALA J 214 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 252 Processing helix chain 'J' and resid 266 through 271 Processing helix chain 'J' and resid 277 through 285 Processing helix chain 'J' and resid 308 through 317 Processing helix chain 'J' and resid 319 through 325 removed outlier: 4.305A pdb=" N ALA J 323 " --> pdb=" O PRO J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 339 Processing helix chain 'J' and resid 343 through 345 No H-bonds generated for 'chain 'J' and resid 343 through 345' Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 351 through 358 Processing helix chain 'J' and resid 360 through 373 removed outlier: 4.080A pdb=" N ALA J 373 " --> pdb=" O GLN J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 430 Processing helix chain 'J' and resid 453 through 460 removed outlier: 3.722A pdb=" N PHE J 457 " --> pdb=" O ASP J 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.707A pdb=" N ILE A 436 " --> pdb=" O ILE A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.574A pdb=" N VAL A 256 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER A 290 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP A 258 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER A 292 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY A 260 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU A 169 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 222 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 171 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 224 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N SER A 173 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 170 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 200 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 172 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 234 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 392 removed outlier: 3.531A pdb=" N LEU A 409 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.876A pdb=" N ILE B 84 " --> pdb=" O ILE B 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.667A pdb=" N GLY B 395 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.589A pdb=" N VAL B 256 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER B 290 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP B 258 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER B 292 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY B 260 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU B 169 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 222 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 171 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS B 224 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER B 173 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL B 170 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 200 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 172 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AB1, first strand: chain 'B' and resid 230 through 234 Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.798A pdb=" N ILE C 84 " --> pdb=" O ILE C 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 150 removed outlier: 4.587A pdb=" N VAL C 256 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER C 290 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP C 258 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER C 292 " --> pdb=" O ASP C 258 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 260 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU C 169 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 222 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 171 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS C 224 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER C 173 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL C 170 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 200 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 172 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AB5, first strand: chain 'C' and resid 386 through 392 removed outlier: 3.969A pdb=" N GLN C 386 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 410 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 444 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.716A pdb=" N ILE D 436 " --> pdb=" O ILE D 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 146 through 150 removed outlier: 4.577A pdb=" N VAL D 256 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER D 290 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP D 258 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER D 292 " --> pdb=" O ASP D 258 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY D 260 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLU D 169 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 222 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 171 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS D 224 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N SER D 173 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL D 170 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL D 200 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 172 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 234 Processing sheet with id=AC1, first strand: chain 'D' and resid 387 through 392 removed outlier: 3.855A pdb=" N MET D 388 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 408 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 444 " --> pdb=" O PHE D 411 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.638A pdb=" N ILE E 436 " --> pdb=" O ILE E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.527A pdb=" N GLY E 395 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 404 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 409 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 146 through 150 removed outlier: 4.566A pdb=" N VAL E 256 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER E 290 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP E 258 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER E 292 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY E 260 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU E 169 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 222 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 171 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS E 224 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER E 173 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL E 170 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL E 200 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 172 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.528A pdb=" N ILE F 436 " --> pdb=" O ILE F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 146 through 150 removed outlier: 4.580A pdb=" N VAL F 256 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER F 290 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP F 258 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER F 292 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY F 260 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU F 169 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 222 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL F 171 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS F 224 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER F 173 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL F 170 " --> pdb=" O HIS F 198 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL F 200 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL F 172 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 179 through 180 Processing sheet with id=AC9, first strand: chain 'F' and resid 230 through 234 Processing sheet with id=AD1, first strand: chain 'F' and resid 387 through 393 removed outlier: 3.568A pdb=" N LEU F 409 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 444 " --> pdb=" O PHE F 411 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 84 through 85 removed outlier: 6.776A pdb=" N ILE G 84 " --> pdb=" O ILE G 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.519A pdb=" N GLY G 395 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 146 through 150 removed outlier: 4.581A pdb=" N VAL G 256 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER G 290 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP G 258 " --> pdb=" O SER G 290 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER G 292 " --> pdb=" O ASP G 258 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY G 260 " --> pdb=" O SER G 292 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU G 169 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU G 222 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL G 171 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS G 224 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER G 173 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL G 170 " --> pdb=" O HIS G 198 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL G 200 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL G 172 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 179 through 180 Processing sheet with id=AD6, first strand: chain 'G' and resid 383 through 391 removed outlier: 3.847A pdb=" N ALA G 384 " --> pdb=" O THR G 412 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR G 412 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN G 386 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 410 " --> pdb=" O GLN G 386 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET G 388 " --> pdb=" O ALA G 408 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA G 408 " --> pdb=" O MET G 388 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 444 " --> pdb=" O PHE G 411 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 84 through 85 removed outlier: 3.609A pdb=" N ILE H 436 " --> pdb=" O ILE H 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 146 through 150 removed outlier: 4.579A pdb=" N VAL H 256 " --> pdb=" O LEU H 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N SER H 290 " --> pdb=" O VAL H 256 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP H 258 " --> pdb=" O SER H 290 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER H 292 " --> pdb=" O ASP H 258 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY H 260 " --> pdb=" O SER H 292 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU H 169 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU H 222 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL H 171 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS H 224 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER H 173 " --> pdb=" O LYS H 224 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL H 170 " --> pdb=" O HIS H 198 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL H 200 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 172 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 179 through 180 Processing sheet with id=AE1, first strand: chain 'H' and resid 230 through 234 Processing sheet with id=AE2, first strand: chain 'H' and resid 386 through 391 removed outlier: 3.515A pdb=" N LEU H 409 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 444 " --> pdb=" O PHE H 411 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 84 through 85 removed outlier: 6.871A pdb=" N ILE I 84 " --> pdb=" O ILE I 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 146 through 150 removed outlier: 4.576A pdb=" N VAL I 256 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER I 290 " --> pdb=" O VAL I 256 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASP I 258 " --> pdb=" O SER I 290 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER I 292 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY I 260 " --> pdb=" O SER I 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU I 169 " --> pdb=" O ALA I 220 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU I 222 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL I 171 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS I 224 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER I 173 " --> pdb=" O LYS I 224 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL I 170 " --> pdb=" O HIS I 198 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL I 200 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL I 172 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 179 through 180 Processing sheet with id=AE6, first strand: chain 'I' and resid 387 through 392 removed outlier: 3.620A pdb=" N LEU I 444 " --> pdb=" O PHE I 411 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.692A pdb=" N ILE J 436 " --> pdb=" O ILE J 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 89 through 91 removed outlier: 6.562A pdb=" N GLY J 395 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU J 409 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU J 444 " --> pdb=" O PHE J 411 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 146 through 150 removed outlier: 4.574A pdb=" N VAL J 256 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER J 290 " --> pdb=" O VAL J 256 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP J 258 " --> pdb=" O SER J 290 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER J 292 " --> pdb=" O ASP J 258 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY J 260 " --> pdb=" O SER J 292 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU J 169 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU J 222 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL J 171 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS J 224 " --> pdb=" O VAL J 171 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER J 173 " --> pdb=" O LYS J 224 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL J 170 " --> pdb=" O HIS J 198 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL J 200 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL J 172 " --> pdb=" O VAL J 200 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 179 through 180 1283 hydrogen bonds defined for protein. 3555 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: 10.17 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.35 - 0.67: 2 0.67 - 0.99: 0 0.99 - 1.31: 4779 1.31 - 1.64: 23645 1.64 - 1.96: 235 Warning: very small bond lengths. Bond restraints: 28661 Sorted by residual: bond pdb=" CG PRO B 389 " pdb=" CD PRO B 389 " ideal model delta sigma weight residual 1.503 0.347 1.156 3.40e-02 8.65e+02 1.16e+03 bond pdb=" CG PRO C 389 " pdb=" CD PRO C 389 " ideal model delta sigma weight residual 1.503 0.587 0.916 3.40e-02 8.65e+02 7.25e+02 bond pdb=" CG PRO F 82 " pdb=" CD PRO F 82 " ideal model delta sigma weight residual 1.503 1.135 0.368 3.40e-02 8.65e+02 1.17e+02 bond pdb=" OP4 LLP F 295 " pdb=" P LLP F 295 " ideal model delta sigma weight residual 1.726 1.538 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" CB PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 1.492 1.959 -0.467 5.00e-02 4.00e+02 8.73e+01 ... (remaining 28656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.79: 38867 9.79 - 19.58: 28 19.58 - 29.37: 5 29.37 - 39.16: 0 39.16 - 48.96: 2 Bond angle restraints: 38902 Sorted by residual: angle pdb=" N PRO B 389 " pdb=" CD PRO B 389 " pdb=" CG PRO B 389 " ideal model delta sigma weight residual 103.20 54.24 48.96 1.50e+00 4.44e-01 1.07e+03 angle pdb=" N PRO C 389 " pdb=" CD PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 103.20 60.72 42.48 1.50e+00 4.44e-01 8.02e+02 angle pdb=" N PRO F 82 " pdb=" CD PRO F 82 " pdb=" CG PRO F 82 " ideal model delta sigma weight residual 103.20 82.33 20.87 1.50e+00 4.44e-01 1.94e+02 angle pdb=" CA PRO C 389 " pdb=" CB PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 104.50 78.17 26.33 1.90e+00 2.77e-01 1.92e+02 angle pdb=" CA PRO B 389 " pdb=" CB PRO B 389 " pdb=" CG PRO B 389 " ideal model delta sigma weight residual 104.50 80.05 24.45 1.90e+00 2.77e-01 1.66e+02 ... (remaining 38897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 16751 30.14 - 60.29: 769 60.29 - 90.43: 67 90.43 - 120.58: 0 120.58 - 150.72: 2 Dihedral angle restraints: 17589 sinusoidal: 6937 harmonic: 10652 Sorted by residual: dihedral pdb=" CA ASP B 402 " pdb=" C ASP B 402 " pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CD LLP B 295 " pdb=" CE LLP B 295 " pdb=" NZ LLP B 295 " pdb=" C4' LLP B 295 " ideal model delta sinusoidal sigma weight residual 249.72 99.00 150.72 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CD LLP F 295 " pdb=" CE LLP F 295 " pdb=" NZ LLP F 295 " pdb=" C4' LLP F 295 " ideal model delta sinusoidal sigma weight residual 249.72 99.07 150.65 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 17586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3039 0.033 - 0.066: 1127 0.066 - 0.099: 299 0.099 - 0.132: 175 0.132 - 0.165: 11 Chirality restraints: 4651 Sorted by residual: chirality pdb=" CA LEU J 297 " pdb=" N LEU J 297 " pdb=" C LEU J 297 " pdb=" CB LEU J 297 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA LEU D 297 " pdb=" N LEU D 297 " pdb=" C LEU D 297 " pdb=" CB LEU D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ASP D 294 " pdb=" N ASP D 294 " pdb=" C ASP D 294 " pdb=" CB ASP D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 4648 not shown) Planarity restraints: 5031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP E 295 " -0.266 2.00e-02 2.50e+03 3.42e-01 1.17e+03 pdb=" NZ LLP E 295 " 0.555 2.00e-02 2.50e+03 pdb=" C4 LLP E 295 " 0.009 2.00e-02 2.50e+03 pdb=" C4' LLP E 295 " -0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 295 " 0.171 2.00e-02 2.50e+03 3.28e-01 1.08e+03 pdb=" NZ LLP B 295 " -0.464 2.00e-02 2.50e+03 pdb=" C4 LLP B 295 " -0.121 2.00e-02 2.50e+03 pdb=" C4' LLP B 295 " 0.414 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP F 295 " -0.160 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" NZ LLP F 295 " 0.447 2.00e-02 2.50e+03 pdb=" C4 LLP F 295 " 0.132 2.00e-02 2.50e+03 pdb=" C4' LLP F 295 " -0.420 2.00e-02 2.50e+03 ... (remaining 5028 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 627 2.69 - 3.24: 26478 3.24 - 3.80: 45882 3.80 - 4.35: 62407 4.35 - 4.90: 104378 Nonbonded interactions: 239772 Sorted by model distance: nonbonded pdb=" OP3 LLP E 295 " pdb=" NH1 ARG F 322 " model vdw 2.141 2.496 nonbonded pdb=" OG SER G 392 " pdb=" OD2 ASP G 447 " model vdw 2.167 3.040 nonbonded pdb=" OG SER B 392 " pdb=" OD2 ASP B 447 " model vdw 2.169 3.040 nonbonded pdb=" NH1 ARG A 322 " pdb=" OP3 LLP B 295 " model vdw 2.175 2.496 nonbonded pdb=" OG SER D 392 " pdb=" OD2 ASP D 447 " model vdw 2.178 3.040 ... (remaining 239767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 77 through 120 or resid 129 through 348 or (resid 349 and \ (name N or name CA or name C or name O or name CB )) or resid 350 through 361 or \ (resid 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 an \ d (name N or name CA or name C or name O or name CB )) or resid 428 through 429 \ or (resid 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 460)) selection = (chain 'B' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 426 or (resid 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 through 429 or (resid 430 and (name N or name CA or name C or na \ me O or name CB )) or resid 431 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'C' and (resid 77 through 120 or resid 129 through 371 or resid 387 throu \ gh 410 or resid 422 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 454 or (resid 455 and (name N or nam \ e CA or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'D' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 426 or (resid 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 through 429 or (resid 430 and (name N or name CA or name C or na \ me O or name CB )) or resid 431 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'E' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 426 or (resid 427 and (name N or name CA o \ r name C or name O or name CB )) or resid 428 through 429 or (resid 430 and (nam \ e N or name CA or name C or name O or name CB )) or resid 431 through 454 or (re \ sid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 th \ rough 460)) selection = (chain 'F' and (resid 77 through 120 or resid 129 through 348 or (resid 349 and \ (name N or name CA or name C or name O or name CB )) or resid 350 through 361 or \ (resid 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 an \ d (name N or name CA or name C or name O or name CB )) or resid 428 through 429 \ or (resid 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 454 or (resid 455 and (name N or name CA or name C or name O or name \ CB )) or resid 456 through 460)) selection = (chain 'G' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 460)) selection = (chain 'H' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 429 or (resid 430 and (name N or name CA or name C or name O or name CB \ )) or resid 431 through 454 or (resid 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 through 460)) selection = (chain 'I' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 429 or (resid 430 and (name N or name CA or name C or name O or name CB \ )) or resid 431 through 454 or (resid 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 through 460)) selection = (chain 'J' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 410 or resid 422 through 429 or (resid 430 \ and (name N or name CA or name C or name O or name CB )) or resid 431 through 4 \ 54 or (resid 455 and (name N or name CA or name C or name O or name CB )) or res \ id 456 through 460)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 63.590 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.012 1.156 28669 Z= 0.436 Angle : 0.859 48.956 38902 Z= 0.459 Chirality : 0.041 0.165 4651 Planarity : 0.011 0.342 5031 Dihedral : 15.672 150.720 10687 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.71 % Allowed : 12.20 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3625 helix: 1.18 (0.14), residues: 1443 sheet: 0.31 (0.23), residues: 472 loop : 0.14 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 445 HIS 0.003 0.001 HIS H 129 PHE 0.015 0.001 PHE G 291 TYR 0.012 0.002 TYR A 230 ARG 0.008 0.001 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.15070 ( 1283) hydrogen bonds : angle 5.98749 ( 3555) covalent geometry : bond 0.01211 (28661) covalent geometry : angle 0.85857 (38902) Misc. bond : bond 0.00239 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 3.228 Fit side-chains REVERT: B 275 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6761 (mm-30) REVERT: C 132 ARG cc_start: 0.7642 (mmp80) cc_final: 0.7432 (mmp80) REVERT: E 275 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6621 (mm-30) REVERT: E 389 PRO cc_start: 0.6695 (Cg_exo) cc_final: 0.6443 (Cg_endo) REVERT: F 132 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7462 (mmp80) REVERT: G 389 PRO cc_start: 0.6833 (Cg_exo) cc_final: 0.6520 (Cg_endo) REVERT: H 389 PRO cc_start: 0.7069 (Cg_exo) cc_final: 0.6834 (Cg_endo) REVERT: H 460 MET cc_start: 0.6143 (mmt) cc_final: 0.5716 (mpt) REVERT: J 403 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7229 (ttm170) outliers start: 21 outliers final: 13 residues processed: 301 average time/residue: 1.4012 time to fit residues: 493.8627 Evaluate side-chains 293 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain J residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 95 optimal weight: 0.0170 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 0.0870 chunk 288 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 214 optimal weight: 0.0270 chunk 334 optimal weight: 0.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 367 GLN F 207 HIS F 226 HIS F 367 GLN G 218 ASN H 226 HIS H 369 GLN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.204300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140048 restraints weight = 29642.537| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.23 r_work: 0.3517 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 28669 Z= 0.106 Angle : 0.531 8.760 38902 Z= 0.257 Chirality : 0.039 0.130 4651 Planarity : 0.004 0.076 5031 Dihedral : 6.898 92.066 4105 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.12 % Allowed : 11.90 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.14), residues: 3625 helix: 1.22 (0.13), residues: 1508 sheet: 0.44 (0.22), residues: 472 loop : 0.13 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 445 HIS 0.003 0.001 HIS G 129 PHE 0.009 0.001 PHE A 291 TYR 0.008 0.001 TYR G 379 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1283) hydrogen bonds : angle 4.96476 ( 3555) covalent geometry : bond 0.00240 (28661) covalent geometry : angle 0.53139 (38902) Misc. bond : bond 0.00061 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 3.074 Fit side-chains REVERT: A 460 MET cc_start: 0.6341 (tpp) cc_final: 0.6050 (tpt) REVERT: B 188 ASP cc_start: 0.7482 (m-30) cc_final: 0.7249 (m-30) REVERT: B 275 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6610 (mm-30) REVERT: B 460 MET cc_start: 0.6365 (tpp) cc_final: 0.6106 (tpt) REVERT: C 217 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6921 (mm-30) REVERT: D 350 LYS cc_start: 0.7045 (mtmt) cc_final: 0.6724 (mtpp) REVERT: E 131 ASP cc_start: 0.6100 (t0) cc_final: 0.5870 (t0) REVERT: E 132 ARG cc_start: 0.6575 (mmp80) cc_final: 0.6336 (mmp80) REVERT: E 275 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6442 (mm-30) REVERT: H 275 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6842 (mm-30) REVERT: H 460 MET cc_start: 0.5914 (mmt) cc_final: 0.5606 (mpt) REVERT: I 188 ASP cc_start: 0.7701 (m-30) cc_final: 0.7456 (m-30) REVERT: I 275 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6001 (mm-30) outliers start: 63 outliers final: 17 residues processed: 343 average time/residue: 1.2849 time to fit residues: 521.4264 Evaluate side-chains 300 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 282 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 116 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 241 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 160 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 GLN G 218 ASN H 369 GLN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.200647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135897 restraints weight = 29537.568| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.17 r_work: 0.3483 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28669 Z= 0.153 Angle : 0.555 11.448 38902 Z= 0.265 Chirality : 0.041 0.174 4651 Planarity : 0.004 0.048 5031 Dihedral : 6.579 97.505 4087 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.52 % Allowed : 12.94 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.14), residues: 3625 helix: 1.23 (0.14), residues: 1500 sheet: 0.44 (0.23), residues: 472 loop : 0.08 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 445 HIS 0.004 0.001 HIS G 129 PHE 0.016 0.001 PHE A 291 TYR 0.013 0.002 TYR I 230 ARG 0.005 0.000 ARG I 132 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 1283) hydrogen bonds : angle 4.85062 ( 3555) covalent geometry : bond 0.00364 (28661) covalent geometry : angle 0.55484 (38902) Misc. bond : bond 0.00137 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 292 time to evaluate : 2.802 Fit side-chains REVERT: A 460 MET cc_start: 0.6414 (tpp) cc_final: 0.6120 (tpt) REVERT: B 132 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.5807 (mmp80) REVERT: B 188 ASP cc_start: 0.7624 (m-30) cc_final: 0.7374 (m-30) REVERT: B 275 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6652 (mm-30) REVERT: B 460 MET cc_start: 0.6326 (tpp) cc_final: 0.6017 (tpt) REVERT: C 217 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: C 274 LYS cc_start: 0.6600 (tmtm) cc_final: 0.6326 (tptp) REVERT: E 217 GLU cc_start: 0.7276 (pm20) cc_final: 0.6833 (mm-30) REVERT: E 275 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6551 (mm-30) REVERT: E 460 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3676 (mmp) REVERT: G 131 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6704 (p0) REVERT: H 136 GLN cc_start: 0.5996 (mm110) cc_final: 0.5796 (tt0) REVERT: H 217 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: H 275 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6816 (mm-30) REVERT: H 460 MET cc_start: 0.5901 (mmt) cc_final: 0.5489 (mpt) REVERT: I 266 ASP cc_start: 0.6431 (t0) cc_final: 0.6228 (t0) outliers start: 75 outliers final: 30 residues processed: 337 average time/residue: 1.2814 time to fit residues: 510.4635 Evaluate side-chains 310 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 204 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 295 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS E 218 ASN E 367 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 GLN G 129 HIS G 218 ASN H 207 HIS ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.196657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131264 restraints weight = 29883.650| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.17 r_work: 0.3431 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 28669 Z= 0.254 Angle : 0.652 13.336 38902 Z= 0.313 Chirality : 0.045 0.170 4651 Planarity : 0.004 0.052 5031 Dihedral : 6.919 106.852 4087 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.86 % Allowed : 14.05 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.14), residues: 3625 helix: 0.91 (0.14), residues: 1489 sheet: 0.29 (0.23), residues: 472 loop : -0.16 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 445 HIS 0.006 0.001 HIS G 129 PHE 0.025 0.002 PHE D 291 TYR 0.018 0.002 TYR I 230 ARG 0.008 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1283) hydrogen bonds : angle 5.02859 ( 3555) covalent geometry : bond 0.00612 (28661) covalent geometry : angle 0.65164 (38902) Misc. bond : bond 0.00257 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 277 time to evaluate : 3.069 Fit side-chains revert: symmetry clash REVERT: A 309 LYS cc_start: 0.7079 (tttp) cc_final: 0.6846 (tttp) REVERT: A 460 MET cc_start: 0.6705 (tpp) cc_final: 0.6447 (tpt) REVERT: B 275 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6682 (mm-30) REVERT: C 217 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: C 274 LYS cc_start: 0.6578 (tmtm) cc_final: 0.6227 (tttp) REVERT: C 343 HIS cc_start: 0.6604 (m-70) cc_final: 0.5933 (t-170) REVERT: D 335 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: E 217 GLU cc_start: 0.7282 (pm20) cc_final: 0.6867 (mm-30) REVERT: E 275 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6547 (mm-30) REVERT: F 217 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: G 110 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: G 461 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6851 (tp) REVERT: H 94 ASN cc_start: 0.6761 (m-40) cc_final: 0.6551 (m-40) REVERT: H 217 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: H 275 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7067 (mm-30) REVERT: J 343 HIS cc_start: 0.6563 (m-70) cc_final: 0.5858 (t-170) outliers start: 85 outliers final: 33 residues processed: 329 average time/residue: 1.3380 time to fit residues: 518.9468 Evaluate side-chains 304 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 402 ASP Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 126 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 352 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 212 optimal weight: 0.7980 chunk 288 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN A 343 HIS ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS E 218 ASN G 218 ASN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.201023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136527 restraints weight = 29685.156| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.22 r_work: 0.3484 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28669 Z= 0.115 Angle : 0.522 9.631 38902 Z= 0.250 Chirality : 0.040 0.137 4651 Planarity : 0.003 0.049 5031 Dihedral : 6.517 97.501 4087 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.72 % Allowed : 14.99 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.14), residues: 3625 helix: 1.18 (0.14), residues: 1498 sheet: 0.27 (0.22), residues: 472 loop : -0.07 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 445 HIS 0.004 0.001 HIS A 343 PHE 0.012 0.001 PHE D 291 TYR 0.010 0.001 TYR H 230 ARG 0.004 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1283) hydrogen bonds : angle 4.75876 ( 3555) covalent geometry : bond 0.00264 (28661) covalent geometry : angle 0.52154 (38902) Misc. bond : bond 0.00097 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 3.050 Fit side-chains REVERT: A 106 GLU cc_start: 0.6605 (tp30) cc_final: 0.6239 (mm-30) REVERT: A 460 MET cc_start: 0.6648 (tpp) cc_final: 0.6380 (tpt) REVERT: B 132 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.5764 (mmp80) REVERT: B 188 ASP cc_start: 0.7369 (m-30) cc_final: 0.7134 (m-30) REVERT: B 275 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6648 (mm-30) REVERT: C 217 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: C 343 HIS cc_start: 0.6427 (m-70) cc_final: 0.5699 (t-170) REVERT: C 350 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6482 (mtmt) REVERT: E 217 GLU cc_start: 0.7264 (pm20) cc_final: 0.6719 (mm-30) REVERT: E 275 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6560 (mm-30) REVERT: E 460 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3471 (mmp) REVERT: F 275 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6893 (mt-10) REVERT: G 131 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6798 (p0) REVERT: H 217 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: H 275 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7003 (mm-30) REVERT: J 343 HIS cc_start: 0.6320 (m-70) cc_final: 0.5573 (t-170) outliers start: 81 outliers final: 26 residues processed: 335 average time/residue: 1.2900 time to fit residues: 510.2960 Evaluate side-chains 299 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 305 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 73 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 347 optimal weight: 0.7980 chunk 321 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 357 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 258 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 367 GLN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.198736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133913 restraints weight = 29645.969| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.17 r_work: 0.3462 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28669 Z= 0.173 Angle : 0.569 11.379 38902 Z= 0.271 Chirality : 0.042 0.223 4651 Planarity : 0.004 0.049 5031 Dihedral : 6.419 101.376 4078 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.59 % Allowed : 15.62 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.14), residues: 3625 helix: 1.16 (0.14), residues: 1490 sheet: 0.26 (0.22), residues: 472 loop : -0.08 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 445 HIS 0.003 0.001 HIS J 207 PHE 0.018 0.002 PHE D 291 TYR 0.014 0.002 TYR I 230 ARG 0.005 0.000 ARG F 132 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 1283) hydrogen bonds : angle 4.80548 ( 3555) covalent geometry : bond 0.00416 (28661) covalent geometry : angle 0.56873 (38902) Misc. bond : bond 0.00170 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 273 time to evaluate : 3.136 Fit side-chains revert: symmetry clash REVERT: A 309 LYS cc_start: 0.7219 (ttmp) cc_final: 0.7016 (ttmm) REVERT: A 460 MET cc_start: 0.6685 (tpp) cc_final: 0.6416 (tpt) REVERT: B 132 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.5887 (mmp80) REVERT: B 188 ASP cc_start: 0.7497 (m-30) cc_final: 0.7266 (m-30) REVERT: B 275 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6669 (mm-30) REVERT: B 388 MET cc_start: 0.5252 (mtt) cc_final: 0.5043 (mtp) REVERT: C 217 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7007 (mm-30) REVERT: C 274 LYS cc_start: 0.6699 (tmtm) cc_final: 0.6458 (tptp) REVERT: C 343 HIS cc_start: 0.6566 (m-70) cc_final: 0.5827 (t-170) REVERT: C 350 LYS cc_start: 0.7160 (mtpp) cc_final: 0.6403 (mtmt) REVERT: E 217 GLU cc_start: 0.7307 (pm20) cc_final: 0.6765 (mm-30) REVERT: E 275 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6552 (mm-30) REVERT: F 217 GLU cc_start: 0.7233 (pm20) cc_final: 0.6641 (mm-30) REVERT: G 131 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6868 (p0) REVERT: G 461 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6908 (tp) REVERT: H 217 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: H 233 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7516 (mm-40) REVERT: H 275 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7127 (mm-30) REVERT: I 188 ASP cc_start: 0.7735 (m-30) cc_final: 0.7499 (m-30) REVERT: J 343 HIS cc_start: 0.6405 (m-70) cc_final: 0.5653 (t-170) outliers start: 77 outliers final: 36 residues processed: 320 average time/residue: 1.2969 time to fit residues: 493.6342 Evaluate side-chains 312 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 337 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS B 129 HIS E 218 ASN G 218 ASN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136637 restraints weight = 29756.504| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.23 r_work: 0.3491 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28669 Z= 0.114 Angle : 0.516 9.377 38902 Z= 0.245 Chirality : 0.040 0.200 4651 Planarity : 0.003 0.049 5031 Dihedral : 6.230 95.467 4078 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.49 % Allowed : 16.06 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.14), residues: 3625 helix: 1.30 (0.14), residues: 1499 sheet: 0.30 (0.22), residues: 466 loop : -0.03 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 445 HIS 0.003 0.000 HIS A 343 PHE 0.012 0.001 PHE B 291 TYR 0.010 0.001 TYR E 230 ARG 0.005 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 1283) hydrogen bonds : angle 4.66760 ( 3555) covalent geometry : bond 0.00270 (28661) covalent geometry : angle 0.51561 (38902) Misc. bond : bond 0.00095 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 2.892 Fit side-chains REVERT: A 309 LYS cc_start: 0.7158 (ttmp) cc_final: 0.6861 (ttmm) REVERT: A 460 MET cc_start: 0.6586 (tpp) cc_final: 0.6348 (tpt) REVERT: B 132 ARG cc_start: 0.7316 (pmt170) cc_final: 0.5824 (mmp80) REVERT: B 188 ASP cc_start: 0.7413 (m-30) cc_final: 0.7167 (m-30) REVERT: B 275 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6660 (mm-30) REVERT: C 217 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: C 274 LYS cc_start: 0.6600 (tmtm) cc_final: 0.6363 (tptp) REVERT: C 343 HIS cc_start: 0.6391 (m-70) cc_final: 0.5660 (t-170) REVERT: C 350 LYS cc_start: 0.7090 (mtpp) cc_final: 0.6335 (mtmt) REVERT: D 350 LYS cc_start: 0.6991 (mtmt) cc_final: 0.6699 (mtpp) REVERT: E 217 GLU cc_start: 0.7285 (pm20) cc_final: 0.6731 (mm-30) REVERT: E 275 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6574 (mm-30) REVERT: E 460 MET cc_start: 0.3883 (OUTLIER) cc_final: 0.3485 (mmp) REVERT: F 217 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6575 (mm-30) REVERT: F 275 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6653 (mm-30) REVERT: G 131 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6811 (p0) REVERT: H 217 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: I 188 ASP cc_start: 0.7652 (m-30) cc_final: 0.7414 (m-30) REVERT: J 343 HIS cc_start: 0.6331 (m-70) cc_final: 0.5588 (t-170) outliers start: 74 outliers final: 40 residues processed: 327 average time/residue: 1.2794 time to fit residues: 493.8475 Evaluate side-chains 308 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 94 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 121 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS E 218 ASN E 367 GLN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134978 restraints weight = 29600.090| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.17 r_work: 0.3476 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28669 Z= 0.142 Angle : 0.544 10.386 38902 Z= 0.258 Chirality : 0.041 0.194 4651 Planarity : 0.003 0.047 5031 Dihedral : 6.288 98.785 4078 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.35 % Allowed : 16.60 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.14), residues: 3625 helix: 1.31 (0.14), residues: 1493 sheet: 0.29 (0.22), residues: 466 loop : -0.02 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 445 HIS 0.003 0.001 HIS H 129 PHE 0.015 0.001 PHE D 291 TYR 0.012 0.001 TYR F 230 ARG 0.006 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 1283) hydrogen bonds : angle 4.69716 ( 3555) covalent geometry : bond 0.00340 (28661) covalent geometry : angle 0.54398 (38902) Misc. bond : bond 0.00133 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 2.953 Fit side-chains REVERT: A 460 MET cc_start: 0.6574 (tpp) cc_final: 0.6312 (tpt) REVERT: B 132 ARG cc_start: 0.7433 (pmt170) cc_final: 0.5978 (mmp80) REVERT: B 188 ASP cc_start: 0.7544 (m-30) cc_final: 0.7309 (m-30) REVERT: B 275 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6677 (mm-30) REVERT: C 217 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: C 274 LYS cc_start: 0.6562 (tmtm) cc_final: 0.6305 (tptp) REVERT: C 343 HIS cc_start: 0.6532 (m-70) cc_final: 0.5789 (t-170) REVERT: C 350 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6412 (mtmt) REVERT: D 350 LYS cc_start: 0.7028 (mtmt) cc_final: 0.6724 (mtpp) REVERT: E 217 GLU cc_start: 0.7338 (pm20) cc_final: 0.6782 (mm-30) REVERT: E 275 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6548 (mm-30) REVERT: E 460 MET cc_start: 0.3977 (OUTLIER) cc_final: 0.3525 (mmp) REVERT: F 217 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: F 275 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6836 (mt-10) REVERT: F 335 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: G 131 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6871 (p0) REVERT: H 217 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: H 233 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: I 188 ASP cc_start: 0.7699 (m-30) cc_final: 0.7450 (m-30) REVERT: J 343 HIS cc_start: 0.6409 (m-70) cc_final: 0.5652 (t-170) outliers start: 70 outliers final: 41 residues processed: 314 average time/residue: 1.3057 time to fit residues: 482.9834 Evaluate side-chains 315 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 242 optimal weight: 0.0060 chunk 48 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 329 optimal weight: 7.9990 chunk 15 optimal weight: 0.0170 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS D 367 GLN E 218 ASN E 367 GLN F 316 GLN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138921 restraints weight = 29802.065| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3511 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28669 Z= 0.093 Angle : 0.495 8.066 38902 Z= 0.235 Chirality : 0.039 0.154 4651 Planarity : 0.003 0.046 5031 Dihedral : 6.062 90.325 4078 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.71 % Allowed : 17.27 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.14), residues: 3625 helix: 1.47 (0.14), residues: 1494 sheet: 0.34 (0.22), residues: 478 loop : 0.04 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 445 HIS 0.002 0.000 HIS A 343 PHE 0.010 0.001 PHE B 291 TYR 0.009 0.001 TYR C 230 ARG 0.005 0.000 ARG F 132 Details of bonding type rmsd hydrogen bonds : bond 0.02577 ( 1283) hydrogen bonds : angle 4.55408 ( 3555) covalent geometry : bond 0.00212 (28661) covalent geometry : angle 0.49461 (38902) Misc. bond : bond 0.00057 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 3.040 Fit side-chains REVERT: A 460 MET cc_start: 0.6539 (tpp) cc_final: 0.6279 (tpt) REVERT: B 132 ARG cc_start: 0.7401 (pmt170) cc_final: 0.5973 (mmp80) REVERT: B 188 ASP cc_start: 0.7435 (m-30) cc_final: 0.7190 (m-30) REVERT: B 275 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6776 (mm-30) REVERT: C 217 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: C 274 LYS cc_start: 0.6413 (tmtm) cc_final: 0.6185 (tptp) REVERT: C 343 HIS cc_start: 0.6415 (m-70) cc_final: 0.5743 (t-170) REVERT: C 350 LYS cc_start: 0.7090 (mtpp) cc_final: 0.6369 (mtmt) REVERT: D 350 LYS cc_start: 0.6928 (mtmt) cc_final: 0.6665 (mtpp) REVERT: D 388 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.4891 (tmt) REVERT: E 217 GLU cc_start: 0.7269 (pm20) cc_final: 0.6716 (mm-30) REVERT: E 275 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6564 (mm-30) REVERT: E 460 MET cc_start: 0.3790 (OUTLIER) cc_final: 0.3420 (mmp) REVERT: F 217 GLU cc_start: 0.7187 (pm20) cc_final: 0.6534 (mm-30) REVERT: F 275 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6680 (mm-30) REVERT: H 209 ASN cc_start: 0.7683 (t0) cc_final: 0.7315 (t0) REVERT: I 188 ASP cc_start: 0.7533 (m-30) cc_final: 0.7280 (m-30) REVERT: J 343 HIS cc_start: 0.6288 (m-70) cc_final: 0.5584 (t-170) outliers start: 51 outliers final: 31 residues processed: 311 average time/residue: 1.2823 time to fit residues: 472.2613 Evaluate side-chains 297 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 297 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 288 optimal weight: 0.6980 chunk 165 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS B 343 HIS E 367 GLN H 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.199466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134707 restraints weight = 29618.242| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.18 r_work: 0.3473 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28669 Z= 0.163 Angle : 0.564 10.829 38902 Z= 0.267 Chirality : 0.041 0.207 4651 Planarity : 0.004 0.046 5031 Dihedral : 6.281 99.933 4078 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.44 % Allowed : 17.84 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.14), residues: 3625 helix: 1.37 (0.14), residues: 1494 sheet: 0.33 (0.22), residues: 473 loop : 0.01 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 445 HIS 0.003 0.001 HIS G 207 PHE 0.017 0.001 PHE D 291 TYR 0.013 0.002 TYR F 230 ARG 0.009 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 1283) hydrogen bonds : angle 4.69013 ( 3555) covalent geometry : bond 0.00398 (28661) covalent geometry : angle 0.56440 (38902) Misc. bond : bond 0.00157 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 3.070 Fit side-chains REVERT: A 460 MET cc_start: 0.6592 (tpp) cc_final: 0.6335 (tpt) REVERT: B 132 ARG cc_start: 0.7476 (pmt170) cc_final: 0.6060 (mmp80) REVERT: B 188 ASP cc_start: 0.7551 (m-30) cc_final: 0.7310 (m-30) REVERT: B 275 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6695 (mm-30) REVERT: C 217 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: C 274 LYS cc_start: 0.6578 (tmtm) cc_final: 0.6312 (tptp) REVERT: C 343 HIS cc_start: 0.6451 (m-70) cc_final: 0.5780 (t-170) REVERT: C 350 LYS cc_start: 0.7196 (mtpp) cc_final: 0.6447 (mtmt) REVERT: D 350 LYS cc_start: 0.7010 (mtmt) cc_final: 0.6729 (mtpp) REVERT: D 388 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.4928 (tmt) REVERT: E 217 GLU cc_start: 0.7324 (pm20) cc_final: 0.6781 (mm-30) REVERT: E 275 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6548 (mm-30) REVERT: E 460 MET cc_start: 0.3918 (OUTLIER) cc_final: 0.3504 (mmp) REVERT: F 217 GLU cc_start: 0.7253 (pm20) cc_final: 0.6626 (mm-30) REVERT: F 275 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6772 (mt-10) REVERT: I 188 ASP cc_start: 0.7711 (m-30) cc_final: 0.7491 (m-30) REVERT: J 343 HIS cc_start: 0.6398 (m-70) cc_final: 0.5626 (t-170) outliers start: 43 outliers final: 30 residues processed: 284 average time/residue: 1.3932 time to fit residues: 464.6646 Evaluate side-chains 288 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 269 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 348 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 112 optimal weight: 0.0040 chunk 34 optimal weight: 4.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 343 HIS D 218 ASN D 316 GLN E 367 GLN G 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.198048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133112 restraints weight = 29685.333| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.17 r_work: 0.3454 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28669 Z= 0.190 Angle : 0.597 11.792 38902 Z= 0.283 Chirality : 0.042 0.215 4651 Planarity : 0.004 0.046 5031 Dihedral : 6.406 104.508 4078 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.65 % Allowed : 17.61 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.14), residues: 3625 helix: 1.22 (0.14), residues: 1490 sheet: 0.28 (0.22), residues: 473 loop : -0.06 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 445 HIS 0.003 0.001 HIS A 343 PHE 0.020 0.002 PHE D 291 TYR 0.014 0.002 TYR I 230 ARG 0.009 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 1283) hydrogen bonds : angle 4.80607 ( 3555) covalent geometry : bond 0.00462 (28661) covalent geometry : angle 0.59685 (38902) Misc. bond : bond 0.00190 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24006.94 seconds wall clock time: 413 minutes 4.86 seconds (24784.86 seconds total)