Starting phenix.real_space_refine on Fri Oct 30 09:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191.map" model { file = "/net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wrm_66191/10_2026/9wrm_66191_neut.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 21994 2.51 5 N 6164 2.21 5 O 6610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34968 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "B" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3492 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "D" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "E" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "F" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "G" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "I" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3498 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Chain: "J" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3492 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 8.98, per 1000 atoms: 0.26 Number of scatterers: 34968 At special positions: 0 Unit cell: (167.2, 137.5, 147.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 6610 8.00 N 6164 7.00 C 21994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8300 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 16 sheets defined 46.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 179 through 200 removed outlier: 4.112A pdb=" N ARG A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 225 through 246 removed outlier: 3.803A pdb=" N LYS A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.621A pdb=" N PHE A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.703A pdb=" N GLN A 394 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 395 " --> pdb=" O ALA A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.657A pdb=" N ARG B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 179 through 200 removed outlier: 3.551A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Proline residue: B 188 - end of helix Processing helix chain 'B' and resid 225 through 246 removed outlier: 3.527A pdb=" N LYS B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 289 through 303 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 313 through 320 removed outlier: 4.016A pdb=" N TYR B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 318 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 320' Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.662A pdb=" N GLN B 394 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 395 " --> pdb=" O ALA B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 179 through 200 removed outlier: 3.687A pdb=" N ARG C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 225 through 246 removed outlier: 3.821A pdb=" N LYS C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 289 through 303 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.886A pdb=" N TYR C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 318 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 319' Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 380 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.634A pdb=" N GLN C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 395 " --> pdb=" O ALA C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'C' and resid 415 through 423 Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 44 through 50 Processing helix chain 'D' and resid 50 through 55 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.689A pdb=" N ARG D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 182 through 200 removed outlier: 3.671A pdb=" N MET D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.723A pdb=" N LYS D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 289 through 303 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.604A pdb=" N ARG D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 315 through 320' Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 362 through 381 Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.566A pdb=" N GLN D 394 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 415 Processing helix chain 'D' and resid 415 through 423 Processing helix chain 'D' and resid 423 through 443 Processing helix chain 'D' and resid 446 through 454 Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 123 through 137 Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 179 through 201 removed outlier: 3.654A pdb=" N ARG E 185 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Proline residue: E 188 - end of helix Processing helix chain 'E' and resid 225 through 246 removed outlier: 3.810A pdb=" N LYS E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 288 Processing helix chain 'E' and resid 289 through 303 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 313 through 319 removed outlier: 3.923A pdb=" N TYR E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS E 318 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 319 " --> pdb=" O ASN E 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 319' Processing helix chain 'E' and resid 346 through 350 Processing helix chain 'E' and resid 362 through 380 Processing helix chain 'E' and resid 391 through 395 removed outlier: 3.604A pdb=" N GLN E 394 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 395 " --> pdb=" O ALA E 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 391 through 395' Processing helix chain 'E' and resid 404 through 415 Processing helix chain 'E' and resid 415 through 423 Processing helix chain 'E' and resid 423 through 443 Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 123 through 138 removed outlier: 3.573A pdb=" N GLN F 131 " --> pdb=" O ILE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 163 Processing helix chain 'F' and resid 182 through 200 removed outlier: 3.645A pdb=" N MET F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Proline residue: F 188 - end of helix removed outlier: 3.809A pdb=" N ASP F 192 " --> pdb=" O PRO F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 246 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 289 through 303 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'F' and resid 313 through 320 removed outlier: 3.973A pdb=" N TYR F 317 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS F 318 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 320' Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 362 through 381 removed outlier: 3.551A pdb=" N GLY F 374 " --> pdb=" O LEU F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 415 Processing helix chain 'F' and resid 415 through 423 Processing helix chain 'F' and resid 423 through 444 Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 44 through 50 Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 93 through 96 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'G' and resid 156 through 163 Processing helix chain 'G' and resid 179 through 200 removed outlier: 3.815A pdb=" N ARG G 185 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Proline residue: G 188 - end of helix Processing helix chain 'G' and resid 225 through 246 removed outlier: 3.654A pdb=" N LYS G 240 " --> pdb=" O LYS G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 289 through 303 Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 313 through 320 removed outlier: 3.896A pdb=" N TYR G 317 " --> pdb=" O THR G 313 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 318 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG G 319 " --> pdb=" O ASN G 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 313 through 320' Processing helix chain 'G' and resid 346 through 350 Processing helix chain 'G' and resid 362 through 381 Processing helix chain 'G' and resid 404 through 415 Processing helix chain 'G' and resid 415 through 423 Processing helix chain 'G' and resid 423 through 444 removed outlier: 3.548A pdb=" N ASN G 433 " --> pdb=" O HIS G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 454 Processing helix chain 'H' and resid 10 through 20 Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 50 through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 123 through 138 removed outlier: 3.505A pdb=" N GLN H 131 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 179 through 200 removed outlier: 3.643A pdb=" N SER H 183 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG H 185 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) Proline residue: H 188 - end of helix removed outlier: 3.705A pdb=" N ASP H 192 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 246 removed outlier: 3.633A pdb=" N LYS H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 288 Processing helix chain 'H' and resid 289 through 303 Processing helix chain 'H' and resid 306 through 311 Processing helix chain 'H' and resid 313 through 320 removed outlier: 3.757A pdb=" N TYR H 317 " --> pdb=" O THR H 313 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE H 320 " --> pdb=" O SER H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 Processing helix chain 'H' and resid 362 through 381 Processing helix chain 'H' and resid 391 through 395 removed outlier: 3.755A pdb=" N GLN H 394 " --> pdb=" O ASN H 391 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 395 " --> pdb=" O ALA H 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 391 through 395' Processing helix chain 'H' and resid 404 through 415 Processing helix chain 'H' and resid 415 through 423 Processing helix chain 'H' and resid 423 through 444 Processing helix chain 'H' and resid 446 through 454 Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 123 through 137 removed outlier: 3.528A pdb=" N GLN I 131 " --> pdb=" O ILE I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 164 Processing helix chain 'I' and resid 179 through 200 removed outlier: 3.562A pdb=" N SER I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG I 185 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET I 186 " --> pdb=" O ALA I 182 " (cutoff:3.500A) Proline residue: I 188 - end of helix removed outlier: 3.678A pdb=" N ASP I 192 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 246 removed outlier: 3.913A pdb=" N LYS I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 288 Processing helix chain 'I' and resid 289 through 303 Processing helix chain 'I' and resid 306 through 311 Processing helix chain 'I' and resid 315 through 319 Processing helix chain 'I' and resid 346 through 350 Processing helix chain 'I' and resid 362 through 381 Processing helix chain 'I' and resid 404 through 415 removed outlier: 3.566A pdb=" N PHE I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU I 413 " --> pdb=" O ALA I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 423 removed outlier: 3.506A pdb=" N ARG I 419 " --> pdb=" O SER I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 423 through 444 Processing helix chain 'I' and resid 446 through 454 Processing helix chain 'J' and resid 10 through 20 Processing helix chain 'J' and resid 44 through 50 Processing helix chain 'J' and resid 50 through 55 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 123 through 138 Processing helix chain 'J' and resid 156 through 163 Processing helix chain 'J' and resid 179 through 186 removed outlier: 3.794A pdb=" N ARG J 185 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET J 186 " --> pdb=" O ALA J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 200 Processing helix chain 'J' and resid 225 through 246 removed outlier: 3.562A pdb=" N ASN J 237 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 288 Processing helix chain 'J' and resid 289 through 303 Processing helix chain 'J' and resid 306 through 311 Processing helix chain 'J' and resid 315 through 320 removed outlier: 3.792A pdb=" N PHE J 320 " --> pdb=" O SER J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 350 Processing helix chain 'J' and resid 362 through 381 Processing helix chain 'J' and resid 391 through 395 removed outlier: 3.684A pdb=" N GLN J 394 " --> pdb=" O ASN J 391 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY J 395 " --> pdb=" O ALA J 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 391 through 395' Processing helix chain 'J' and resid 404 through 415 Processing helix chain 'J' and resid 415 through 423 Processing helix chain 'J' and resid 423 through 444 Processing helix chain 'J' and resid 446 through 454 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 43 removed outlier: 6.492A pdb=" N THR A 25 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL A 108 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A 27 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 110 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 29 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU A 112 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N THR A 31 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 12.102A pdb=" N THR A 105 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N LEU A 96 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N LEU A 107 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N SER A 94 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A 109 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 113 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 153 current: chain 'A' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 215 through 220 current: chain 'A' and resid 341 through 344 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 37 through 43 current: chain 'B' and resid 86 through 98 removed outlier: 4.437A pdb=" N ILE B 109 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER B 94 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N LEU B 107 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N LEU B 96 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N THR B 105 " --> pdb=" O LEU B 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 105 through 113 current: chain 'C' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 215 through 220 current: chain 'C' and resid 341 through 344 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 153 current: chain 'B' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 215 through 220 current: chain 'B' and resid 341 through 344 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.670A pdb=" N THR C 25 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL C 108 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE C 27 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA C 110 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA C 29 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 112 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N THR C 31 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 12.515A pdb=" N THR C 105 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N LEU C 96 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N LEU C 107 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N SER C 94 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 109 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 37 through 43 current: chain 'D' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 86 through 91 current: chain 'D' and resid 105 through 113 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 105 through 113 current: chain 'E' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 215 through 220 current: chain 'E' and resid 341 through 344 Processing sheet with id=AA7, first strand: chain 'D' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 153 current: chain 'D' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 220 current: chain 'D' and resid 341 through 344 Processing sheet with id=AA8, first strand: chain 'E' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 37 through 43 current: chain 'E' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 86 through 91 current: chain 'E' and resid 105 through 113 Processing sheet with id=AA9, first strand: chain 'F' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 37 through 43 current: chain 'F' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 86 through 91 current: chain 'F' and resid 105 through 113 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 105 through 113 current: chain 'G' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 215 through 220 current: chain 'G' and resid 341 through 344 Processing sheet with id=AB1, first strand: chain 'F' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 140 through 153 current: chain 'F' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 215 through 220 current: chain 'F' and resid 339 through 344 Processing sheet with id=AB2, first strand: chain 'G' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 37 through 43 current: chain 'G' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 86 through 91 current: chain 'G' and resid 105 through 113 Processing sheet with id=AB3, first strand: chain 'H' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 37 through 43 current: chain 'H' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 86 through 91 current: chain 'H' and resid 105 through 113 Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 153 current: chain 'H' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 215 through 220 current: chain 'H' and resid 341 through 344 Processing sheet with id=AB5, first strand: chain 'I' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 37 through 43 current: chain 'I' and resid 86 through 91 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 86 through 91 current: chain 'I' and resid 105 through 113 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 105 through 113 current: chain 'J' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 215 through 220 current: chain 'J' and resid 341 through 344 Processing sheet with id=AB6, first strand: chain 'I' and resid 140 through 153 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 140 through 153 current: chain 'I' and resid 215 through 220 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 215 through 220 current: chain 'I' and resid 341 through 344 Processing sheet with id=AB7, first strand: chain 'J' and resid 37 through 43 removed outlier: 5.681A pdb=" N THR J 31 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU J 112 " --> pdb=" O THR J 31 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N THR J 105 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LEU J 96 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N LEU J 107 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER J 94 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE J 109 " --> pdb=" O ASP J 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL J 56 " --> pdb=" O MET J 89 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9887 1.33 - 1.45: 6148 1.45 - 1.57: 19343 1.57 - 1.69: 0 1.69 - 1.81: 310 Bond restraints: 35688 Sorted by residual: bond pdb=" CB MET E 87 " pdb=" CG MET E 87 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CA ASN I 262 " pdb=" CB ASN I 262 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.35e-02 5.49e+03 2.47e+00 bond pdb=" C GLY I 261 " pdb=" O GLY I 261 " ideal model delta sigma weight residual 1.230 1.213 0.018 1.21e-02 6.83e+03 2.12e+00 bond pdb=" CA VAL B 356 " pdb=" CB VAL B 356 " ideal model delta sigma weight residual 1.534 1.544 -0.010 6.80e-03 2.16e+04 2.10e+00 bond pdb=" CD GLU I 149 " pdb=" OE2 GLU I 149 " ideal model delta sigma weight residual 1.249 1.276 -0.027 1.90e-02 2.77e+03 2.04e+00 ... (remaining 35683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 47770 2.01 - 4.02: 614 4.02 - 6.03: 90 6.03 - 8.04: 17 8.04 - 10.06: 5 Bond angle restraints: 48496 Sorted by residual: angle pdb=" C ARG E 355 " pdb=" N VAL E 356 " pdb=" CA VAL E 356 " ideal model delta sigma weight residual 120.33 123.13 -2.80 8.00e-01 1.56e+00 1.22e+01 angle pdb=" C ARG C 355 " pdb=" N VAL C 356 " pdb=" CA VAL C 356 " ideal model delta sigma weight residual 120.33 123.09 -2.76 8.00e-01 1.56e+00 1.19e+01 angle pdb=" C ARG G 355 " pdb=" N VAL G 356 " pdb=" CA VAL G 356 " ideal model delta sigma weight residual 120.33 122.92 -2.59 8.00e-01 1.56e+00 1.05e+01 angle pdb=" C ARG I 355 " pdb=" N VAL I 356 " pdb=" CA VAL I 356 " ideal model delta sigma weight residual 120.33 122.86 -2.53 8.00e-01 1.56e+00 9.99e+00 angle pdb=" C ARG A 355 " pdb=" N VAL A 356 " pdb=" CA VAL A 356 " ideal model delta sigma weight residual 120.24 122.22 -1.98 6.30e-01 2.52e+00 9.87e+00 ... (remaining 48491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19928 17.99 - 35.97: 973 35.97 - 53.96: 139 53.96 - 71.95: 45 71.95 - 89.93: 35 Dihedral angle restraints: 21120 sinusoidal: 8100 harmonic: 13020 Sorted by residual: dihedral pdb=" CA ALA F 179 " pdb=" C ALA F 179 " pdb=" N ILE F 180 " pdb=" CA ILE F 180 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU G 455 " pdb=" C GLU G 455 " pdb=" N ARG G 456 " pdb=" CA ARG G 456 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP E 50 " pdb=" C ASP E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 21117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4114 0.044 - 0.087: 993 0.087 - 0.131: 260 0.131 - 0.174: 9 0.174 - 0.218: 4 Chirality restraints: 5380 Sorted by residual: chirality pdb=" CB ILE C 99 " pdb=" CA ILE C 99 " pdb=" CG1 ILE C 99 " pdb=" CG2 ILE C 99 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 371 " pdb=" CA ILE A 371 " pdb=" CG1 ILE A 371 " pdb=" CG2 ILE A 371 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE J 371 " pdb=" CA ILE J 371 " pdb=" CG1 ILE J 371 " pdb=" CG2 ILE J 371 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 5377 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 448 " 0.021 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP J 448 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP J 448 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP J 448 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP J 448 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP J 448 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP J 448 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 448 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 448 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP J 448 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 114 " 0.017 2.00e-02 2.50e+03 1.77e-02 7.85e+00 pdb=" CG TRP I 114 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP I 114 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP I 114 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP I 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP I 114 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 114 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 114 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 114 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP I 114 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 319 " -0.208 9.50e-02 1.11e+02 9.33e-02 5.35e+00 pdb=" NE ARG J 319 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG J 319 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG J 319 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 319 " -0.008 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2014 2.73 - 3.27: 38357 3.27 - 3.82: 62587 3.82 - 4.36: 75904 4.36 - 4.90: 123394 Nonbonded interactions: 302256 Sorted by model distance: nonbonded pdb=" NZ LYS C 40 " pdb=" O ARG C 41 " model vdw 2.189 3.120 nonbonded pdb=" NH1 ARG F 191 " pdb=" OD2 ASP J 24 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG C 304 " pdb=" O ARG C 400 " model vdw 2.199 3.120 nonbonded pdb=" O CYS H 58 " pdb=" N MET H 87 " model vdw 2.203 3.120 nonbonded pdb=" NH1 ARG G 304 " pdb=" O ARG G 400 " model vdw 2.213 3.120 ... (remaining 302251 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'D' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'E' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'F' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'G' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'H' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = (chain 'I' and (resid 1 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 457)) selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.410 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.003 0.056 35688 Z= 0.133 Angle : 0.600 10.056 48496 Z= 0.329 Chirality : 0.040 0.218 5380 Planarity : 0.004 0.093 6408 Dihedral : 11.862 89.934 12820 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.03 % Allowed : 0.03 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4550 helix: 1.61 (0.12), residues: 1680 sheet: -0.59 (0.17), residues: 880 loop : 1.17 (0.16), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 452 TYR 0.018 0.001 TYR I 157 PHE 0.019 0.002 PHE H 47 TRP 0.047 0.002 TRP I 114 HIS 0.010 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (35688) covalent geometry : angle 0.59992 / 0.33 (48496) hydrogen bonds : bond 0.19941 / 13.10 ( 1401) hydrogen bonds : angle 6.77916 / 4.96 ( 3990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9514 (t80) cc_final: 0.9230 (t80) REVERT: A 240 LYS cc_start: 0.9342 (mmmt) cc_final: 0.8715 (mmtt) REVERT: A 250 LEU cc_start: 0.9070 (pt) cc_final: 0.8251 (pt) REVERT: A 264 CYS cc_start: 0.8569 (p) cc_final: 0.8360 (p) REVERT: B 253 MET cc_start: 0.8254 (ppp) cc_final: 0.8048 (ppp) REVERT: B 264 CYS cc_start: 0.8381 (m) cc_final: 0.8072 (m) REVERT: C 232 HIS cc_start: 0.9838 (t-90) cc_final: 0.9249 (t-90) REVERT: C 253 MET cc_start: 0.8759 (ttm) cc_final: 0.8434 (ttm) REVERT: C 264 CYS cc_start: 0.9414 (t) cc_final: 0.9052 (m) REVERT: C 437 GLU cc_start: 0.9091 (tt0) cc_final: 0.8777 (mt-10) REVERT: D 14 LEU cc_start: 0.9789 (tp) cc_final: 0.9488 (tp) REVERT: D 97 ARG cc_start: 0.9149 (ptp-170) cc_final: 0.8761 (ptp-170) REVERT: D 186 MET cc_start: 0.8363 (mpp) cc_final: 0.7920 (mpp) REVERT: D 193 ILE cc_start: 0.9433 (mm) cc_final: 0.9063 (mm) REVERT: E 183 SER cc_start: 0.9715 (t) cc_final: 0.9474 (t) REVERT: E 193 ILE cc_start: 0.9674 (mt) cc_final: 0.9353 (mt) REVERT: E 268 VAL cc_start: 0.9720 (t) cc_final: 0.9450 (p) REVERT: E 295 PHE cc_start: 0.9565 (t80) cc_final: 0.9330 (t80) REVERT: E 354 CYS cc_start: 0.9486 (t) cc_final: 0.9276 (t) REVERT: F 33 MET cc_start: 0.8815 (mmp) cc_final: 0.8343 (mmp) REVERT: G 87 MET cc_start: 0.7866 (tpp) cc_final: 0.6122 (mmm) REVERT: G 89 MET cc_start: 0.9179 (ttm) cc_final: 0.8838 (ttt) REVERT: G 288 MET cc_start: 0.8159 (ptm) cc_final: 0.7654 (ptm) REVERT: H 87 MET cc_start: 0.7848 (tpp) cc_final: 0.7640 (mmm) REVERT: H 229 CYS cc_start: 0.9853 (m) cc_final: 0.9635 (m) REVERT: H 288 MET cc_start: 0.7988 (ptm) cc_final: 0.7588 (ptm) REVERT: H 295 PHE cc_start: 0.9704 (t80) cc_final: 0.9358 (t80) REVERT: I 58 CYS cc_start: 0.8372 (m) cc_final: 0.7561 (m) REVERT: I 89 MET cc_start: 0.9481 (mmp) cc_final: 0.9204 (mmp) REVERT: I 213 MET cc_start: -0.1302 (ttt) cc_final: -0.1790 (tmm) REVERT: I 236 LYS cc_start: 0.9708 (ttmm) cc_final: 0.9497 (mmmm) REVERT: I 291 MET cc_start: 0.8832 (ptm) cc_final: 0.8096 (ppp) REVERT: I 306 PHE cc_start: 0.9280 (m-10) cc_final: 0.8875 (m-10) REVERT: I 354 CYS cc_start: 0.9361 (t) cc_final: 0.9006 (t) REVERT: I 437 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8801 (mm-30) REVERT: J 13 GLU cc_start: 0.9370 (tp30) cc_final: 0.9070 (tp30) REVERT: J 197 MET cc_start: 0.9579 (mmt) cc_final: 0.9374 (mmt) REVERT: J 264 CYS cc_start: 0.8376 (m) cc_final: 0.7792 (m) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.2106 time to fit residues: 144.6574 Evaluate side-chains 306 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 0.0770 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.0570 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 overall best weight: 2.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 231 ASN D 299 GLN E 245 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 GLN ** J 232 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 = 0.3656 r_free = 0.3656 target = 0.070364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049109 restraints weight = 219916.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050178 restraints weight = 185002.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050939 restraints weight = 163065.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051508 restraints weight = 149028.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051752 restraints weight = 139599.008| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35688 Z= 0.127 Angle : 0.538 6.920 48496 Z= 0.286 Chirality : 0.040 0.169 5380 Planarity : 0.004 0.050 6408 Dihedral : 4.322 24.658 5068 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4550 helix: 1.47 (0.12), residues: 1830 sheet: -0.44 (0.17), residues: 930 loop : 1.17 (0.16), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 452 TYR 0.015 0.001 TYR D 61 PHE 0.018 0.001 PHE J 306 TRP 0.025 0.001 TRP E 448 HIS 0.006 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (35688) covalent geometry : angle 0.53831 / 0.29 (48496) hydrogen bonds : bond 0.04685 / 3.13 ( 1401) hydrogen bonds : angle 5.22159 / 3.81 ( 3990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 396 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9574 (t80) cc_final: 0.9257 (t80) REVERT: A 240 LYS cc_start: 0.9349 (mmmt) cc_final: 0.8807 (mmtt) REVERT: A 260 GLU cc_start: 0.8157 (mp0) cc_final: 0.7715 (mm-30) REVERT: A 264 CYS cc_start: 0.8569 (p) cc_final: 0.8366 (p) REVERT: A 288 MET cc_start: 0.7369 (pmm) cc_final: 0.6662 (pmm) REVERT: B 253 MET cc_start: 0.8216 (ppp) cc_final: 0.7925 (ppp) REVERT: B 264 CYS cc_start: 0.8433 (m) cc_final: 0.8027 (m) REVERT: B 288 MET cc_start: 0.7581 (pmm) cc_final: 0.7270 (pmm) REVERT: C 213 MET cc_start: -0.2383 (mmt) cc_final: -0.2867 (mmp) REVERT: C 232 HIS cc_start: 0.9821 (t-90) cc_final: 0.9178 (t-90) REVERT: C 253 MET cc_start: 0.8916 (ttm) cc_final: 0.8480 (ttm) REVERT: C 264 CYS cc_start: 0.9377 (t) cc_final: 0.9058 (t) REVERT: C 437 GLU cc_start: 0.9074 (tt0) cc_final: 0.8797 (mt-10) REVERT: D 14 LEU cc_start: 0.9789 (tp) cc_final: 0.9501 (tp) REVERT: D 77 MET cc_start: 0.6831 (mmp) cc_final: 0.6483 (ppp) REVERT: D 186 MET cc_start: 0.8450 (mpp) cc_final: 0.8186 (mpp) REVERT: D 193 ILE cc_start: 0.9448 (mm) cc_final: 0.9217 (mm) REVERT: E 87 MET cc_start: 0.7341 (tpt) cc_final: 0.6550 (tpt) REVERT: E 193 ILE cc_start: 0.9748 (mt) cc_final: 0.9388 (mt) REVERT: E 236 LYS cc_start: 0.9735 (tttt) cc_final: 0.9301 (tptt) REVERT: E 268 VAL cc_start: 0.9638 (t) cc_final: 0.9298 (p) REVERT: E 288 MET cc_start: 0.9157 (pmm) cc_final: 0.8921 (pmm) REVERT: E 295 PHE cc_start: 0.9588 (t80) cc_final: 0.9324 (t80) REVERT: E 354 CYS cc_start: 0.9462 (t) cc_final: 0.9259 (t) REVERT: F 33 MET cc_start: 0.8737 (mmp) cc_final: 0.8495 (mmm) REVERT: G 87 MET cc_start: 0.8375 (tpp) cc_final: 0.7095 (mmm) REVERT: G 89 MET cc_start: 0.9075 (ttm) cc_final: 0.8740 (ttt) REVERT: H 193 ILE cc_start: 0.9949 (OUTLIER) cc_final: 0.9688 (mm) REVERT: H 288 MET cc_start: 0.8438 (ptm) cc_final: 0.8087 (ptm) REVERT: H 295 PHE cc_start: 0.9696 (t80) cc_final: 0.9346 (t80) REVERT: I 58 CYS cc_start: 0.8595 (m) cc_final: 0.7622 (m) REVERT: I 89 MET cc_start: 0.9492 (mmp) cc_final: 0.9151 (mmp) REVERT: I 153 PHE cc_start: 0.9531 (m-80) cc_final: 0.9302 (m-80) REVERT: I 236 LYS cc_start: 0.9803 (ttmm) cc_final: 0.9489 (mmmm) REVERT: I 288 MET cc_start: 0.7169 (ptp) cc_final: 0.6853 (ptm) REVERT: I 291 MET cc_start: 0.8780 (ptm) cc_final: 0.8045 (ppp) REVERT: I 437 GLU cc_start: 0.9472 (mm-30) cc_final: 0.8944 (mm-30) REVERT: J 13 GLU cc_start: 0.9474 (tp30) cc_final: 0.9134 (tp30) REVERT: J 264 CYS cc_start: 0.8465 (m) cc_final: 0.7861 (m) outliers start: 4 outliers final: 0 residues processed: 398 average time/residue: 0.2022 time to fit residues: 133.6267 Evaluate side-chains 283 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [26, 306, 247, 5, 317, 332, 253, 57, 145, 37, 97] chunk 26 optimal weight: 40.0000 chunk 306 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 332 optimal weight: 0.7980 chunk 253 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 97 optimal weight: 40.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 175 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 286 HIS ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045095 restraints weight = 233200.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.046006 restraints weight = 195637.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046596 restraints weight = 174529.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046959 restraints weight = 160708.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046959 restraints weight = 149394.835| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35688 Z= 0.208 Angle : 0.610 8.439 48496 Z= 0.322 Chirality : 0.041 0.364 5380 Planarity : 0.004 0.064 6408 Dihedral : 4.417 21.013 5068 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.17 % Allowed : 3.15 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4550 helix: 1.19 (0.12), residues: 1850 sheet: -0.39 (0.19), residues: 780 loop : 0.71 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 125 TYR 0.021 0.002 TYR E 235 PHE 0.021 0.002 PHE G 454 TRP 0.029 0.002 TRP C 114 HIS 0.008 0.002 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (35688) covalent geometry : angle 0.60965 / 0.32 (48496) hydrogen bonds : bond 0.04307 / 2.90 ( 1401) hydrogen bonds : angle 5.01318 / 3.64 ( 3990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 347 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9639 (t80) cc_final: 0.9222 (t80) REVERT: A 240 LYS cc_start: 0.9618 (mmtm) cc_final: 0.9299 (mmmt) REVERT: A 260 GLU cc_start: 0.8357 (mp0) cc_final: 0.7899 (mm-30) REVERT: A 264 CYS cc_start: 0.8772 (p) cc_final: 0.8551 (p) REVERT: A 288 MET cc_start: 0.7814 (pmm) cc_final: 0.6874 (pmm) REVERT: B 240 LYS cc_start: 0.9801 (mtmm) cc_final: 0.9401 (mmmm) REVERT: B 253 MET cc_start: 0.8504 (ppp) cc_final: 0.8045 (ppp) REVERT: B 264 CYS cc_start: 0.8492 (m) cc_final: 0.8065 (m) REVERT: B 288 MET cc_start: 0.8435 (pmm) cc_final: 0.7830 (pmm) REVERT: C 89 MET cc_start: 0.9420 (mpp) cc_final: 0.9057 (mpp) REVERT: C 213 MET cc_start: -0.1686 (mmt) cc_final: -0.2019 (mmt) REVERT: C 232 HIS cc_start: 0.9796 (t-90) cc_final: 0.9148 (t-90) REVERT: C 253 MET cc_start: 0.9136 (ttm) cc_final: 0.8345 (ttm) REVERT: C 264 CYS cc_start: 0.9499 (t) cc_final: 0.9230 (t) REVERT: C 310 TYR cc_start: 0.9017 (m-80) cc_final: 0.7993 (m-80) REVERT: D 14 LEU cc_start: 0.9806 (tp) cc_final: 0.9564 (tp) REVERT: D 186 MET cc_start: 0.8837 (mpp) cc_final: 0.8525 (mpp) REVERT: D 190 LEU cc_start: 0.9699 (mt) cc_final: 0.9378 (pp) REVERT: D 229 CYS cc_start: 0.9712 (m) cc_final: 0.9459 (m) REVERT: D 232 HIS cc_start: 0.9779 (t-90) cc_final: 0.9404 (t-90) REVERT: D 253 MET cc_start: 0.8808 (ttm) cc_final: 0.8398 (ttm) REVERT: D 299 GLN cc_start: 0.9402 (mm-40) cc_final: 0.9041 (mm110) REVERT: E 87 MET cc_start: 0.7865 (tpt) cc_final: 0.6949 (tpt) REVERT: E 232 HIS cc_start: 0.9752 (t-90) cc_final: 0.9407 (t-90) REVERT: E 253 MET cc_start: 0.9355 (ttm) cc_final: 0.8940 (ttm) REVERT: E 295 PHE cc_start: 0.9621 (t80) cc_final: 0.9420 (t80) REVERT: F 33 MET cc_start: 0.8650 (mmp) cc_final: 0.8389 (mmm) REVERT: F 193 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9041 (mm) REVERT: F 197 MET cc_start: 0.9451 (mmt) cc_final: 0.9014 (mmm) REVERT: G 87 MET cc_start: 0.8683 (tpp) cc_final: 0.7215 (mmm) REVERT: G 89 MET cc_start: 0.9281 (ttm) cc_final: 0.8971 (ttt) REVERT: G 197 MET cc_start: 0.9276 (mmm) cc_final: 0.9060 (mmt) REVERT: H 1 MET cc_start: 0.3960 (tpt) cc_final: 0.3621 (tpt) REVERT: H 193 ILE cc_start: 0.9915 (OUTLIER) cc_final: 0.9701 (mm) REVERT: H 229 CYS cc_start: 0.9818 (m) cc_final: 0.9549 (p) REVERT: H 288 MET cc_start: 0.8882 (ptm) cc_final: 0.8681 (ttp) REVERT: H 295 PHE cc_start: 0.9693 (t80) cc_final: 0.9421 (t80) REVERT: H 303 LEU cc_start: 0.9485 (tt) cc_final: 0.9276 (mt) REVERT: I 58 CYS cc_start: 0.8791 (m) cc_final: 0.7896 (m) REVERT: I 89 MET cc_start: 0.9523 (mmp) cc_final: 0.9207 (mmp) REVERT: I 236 LYS cc_start: 0.9829 (ttmm) cc_final: 0.9379 (ttmm) REVERT: I 240 LYS cc_start: 0.9590 (mppt) cc_final: 0.9316 (mmtt) REVERT: I 288 MET cc_start: 0.7326 (ptp) cc_final: 0.6967 (ptm) REVERT: I 291 MET cc_start: 0.8802 (ptm) cc_final: 0.8124 (ppp) REVERT: I 306 PHE cc_start: 0.9313 (m-10) cc_final: 0.9041 (m-10) REVERT: I 401 LEU cc_start: 0.8528 (pt) cc_final: 0.8289 (mm) REVERT: J 236 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8862 (mtmm) REVERT: J 288 MET cc_start: 0.8329 (ptt) cc_final: 0.8098 (ptm) outliers start: 6 outliers final: 0 residues processed: 352 average time/residue: 0.2102 time to fit residues: 122.5467 Evaluate side-chains 266 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [335, 123, 114, 396, 430, 401, 315, 126, 22, 39, 344] chunk 335 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 396 optimal weight: 6.9990 chunk 430 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 chunk 315 optimal weight: 30.0000 chunk 126 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 344 optimal weight: 20.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044755 restraints weight = 234760.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045675 restraints weight = 197741.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.046327 restraints weight = 173964.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046640 restraints weight = 160026.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047111 restraints weight = 151231.716| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35688 Z= 0.170 Angle : 0.543 6.759 48496 Z= 0.289 Chirality : 0.040 0.247 5380 Planarity : 0.004 0.043 6408 Dihedral : 4.284 24.389 5068 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.08 % Allowed : 2.56 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4550 helix: 1.37 (0.12), residues: 1830 sheet: -0.57 (0.19), residues: 790 loop : 0.71 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG I 259 TYR 0.017 0.002 TYR H 174 PHE 0.016 0.001 PHE J 306 TRP 0.020 0.001 TRP D 101 HIS 0.009 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (35688) covalent geometry : angle 0.54285 / 0.29 (48496) hydrogen bonds : bond 0.03813 / 2.58 ( 1401) hydrogen bonds : angle 4.89518 / 3.55 ( 3990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 328 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9664 (t80) cc_final: 0.9252 (t80) REVERT: A 240 LYS cc_start: 0.9546 (mmtm) cc_final: 0.9320 (mmtt) REVERT: A 260 GLU cc_start: 0.8474 (mp0) cc_final: 0.8197 (mm-30) REVERT: A 264 CYS cc_start: 0.8792 (p) cc_final: 0.8576 (p) REVERT: A 288 MET cc_start: 0.7790 (pmm) cc_final: 0.7111 (pmm) REVERT: B 89 MET cc_start: 0.8967 (ttt) cc_final: 0.8678 (ttm) REVERT: B 240 LYS cc_start: 0.9781 (mtmm) cc_final: 0.9331 (mmmm) REVERT: B 253 MET cc_start: 0.8498 (ppp) cc_final: 0.8058 (ppp) REVERT: B 264 CYS cc_start: 0.8514 (m) cc_final: 0.8079 (m) REVERT: B 288 MET cc_start: 0.8404 (pmm) cc_final: 0.7824 (pmm) REVERT: C 213 MET cc_start: -0.1578 (mmt) cc_final: -0.1982 (mmt) REVERT: C 253 MET cc_start: 0.9138 (ttm) cc_final: 0.8334 (ttm) REVERT: C 264 CYS cc_start: 0.9499 (t) cc_final: 0.9277 (t) REVERT: C 288 MET cc_start: 0.8666 (ptm) cc_final: 0.8459 (ttp) REVERT: D 14 LEU cc_start: 0.9825 (tp) cc_final: 0.9615 (tp) REVERT: D 186 MET cc_start: 0.8905 (mpp) cc_final: 0.8629 (mpp) REVERT: D 190 LEU cc_start: 0.9710 (mt) cc_final: 0.9368 (pp) REVERT: D 229 CYS cc_start: 0.9666 (m) cc_final: 0.9432 (m) REVERT: D 232 HIS cc_start: 0.9806 (t-90) cc_final: 0.9457 (t-90) REVERT: D 253 MET cc_start: 0.8813 (ttm) cc_final: 0.8391 (ttm) REVERT: E 87 MET cc_start: 0.7909 (tpt) cc_final: 0.7551 (tpp) REVERT: E 107 LEU cc_start: 0.9722 (mt) cc_final: 0.9402 (mp) REVERT: E 232 HIS cc_start: 0.9764 (t-90) cc_final: 0.9422 (t-90) REVERT: E 253 MET cc_start: 0.9392 (ttm) cc_final: 0.8948 (ttm) REVERT: E 295 PHE cc_start: 0.9638 (t80) cc_final: 0.9415 (t80) REVERT: F 193 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9062 (mm) REVERT: F 197 MET cc_start: 0.9450 (mmt) cc_final: 0.9093 (mmm) REVERT: F 253 MET cc_start: 0.8520 (mtt) cc_final: 0.8241 (mmm) REVERT: G 77 MET cc_start: 0.7105 (ppp) cc_final: 0.6867 (ppp) REVERT: G 87 MET cc_start: 0.8749 (tpp) cc_final: 0.7217 (mmm) REVERT: G 89 MET cc_start: 0.9340 (ttm) cc_final: 0.9013 (ttt) REVERT: G 197 MET cc_start: 0.9363 (mmm) cc_final: 0.9109 (mmt) REVERT: G 288 MET cc_start: 0.8778 (ppp) cc_final: 0.8306 (ppp) REVERT: H 14 LEU cc_start: 0.9894 (tp) cc_final: 0.9688 (tp) REVERT: H 193 ILE cc_start: 0.9923 (OUTLIER) cc_final: 0.9720 (pt) REVERT: H 218 ILE cc_start: 0.9386 (mt) cc_final: 0.9180 (tp) REVERT: H 295 PHE cc_start: 0.9685 (t80) cc_final: 0.9397 (t80) REVERT: H 303 LEU cc_start: 0.9463 (tt) cc_final: 0.9263 (mt) REVERT: H 448 TRP cc_start: 0.9536 (t-100) cc_final: 0.9312 (t-100) REVERT: I 58 CYS cc_start: 0.8815 (m) cc_final: 0.7955 (m) REVERT: I 89 MET cc_start: 0.9507 (mmp) cc_final: 0.9229 (mmp) REVERT: I 232 HIS cc_start: 0.9441 (t70) cc_final: 0.9225 (t-170) REVERT: I 236 LYS cc_start: 0.9801 (ttmm) cc_final: 0.9074 (mmmm) REVERT: I 240 LYS cc_start: 0.9701 (mptt) cc_final: 0.9191 (mmtt) REVERT: I 288 MET cc_start: 0.7180 (ptp) cc_final: 0.6677 (ptm) REVERT: I 291 MET cc_start: 0.8907 (ptm) cc_final: 0.8240 (ppp) REVERT: I 306 PHE cc_start: 0.9312 (m-10) cc_final: 0.9088 (m-10) REVERT: I 401 LEU cc_start: 0.8684 (pt) cc_final: 0.8393 (mm) REVERT: J 216 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8262 (mm-40) REVERT: J 288 MET cc_start: 0.8377 (ptt) cc_final: 0.8144 (ptm) REVERT: J 291 MET cc_start: 0.8991 (ppp) cc_final: 0.8742 (ppp) outliers start: 3 outliers final: 0 residues processed: 330 average time/residue: 0.2142 time to fit residues: 115.7905 Evaluate side-chains 253 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [313, 244, 284, 35, 382, 427, 108, 4, 135, 2, 57] chunk 313 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS B 246 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 HIS H 433 ASN ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.064104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044222 restraints weight = 239436.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045159 restraints weight = 199979.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.045834 restraints weight = 176010.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.046320 restraints weight = 161418.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046699 restraints weight = 151699.237| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35688 Z= 0.156 Angle : 0.531 6.750 48496 Z= 0.281 Chirality : 0.040 0.196 5380 Planarity : 0.004 0.061 6408 Dihedral : 4.184 23.166 5068 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.08 % Allowed : 1.84 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4550 helix: 1.44 (0.12), residues: 1830 sheet: -0.45 (0.19), residues: 780 loop : 0.61 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 158 TYR 0.016 0.002 TYR B 430 PHE 0.014 0.001 PHE I 295 TRP 0.015 0.001 TRP E 101 HIS 0.005 0.001 HIS E 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (35688) covalent geometry : angle 0.53054 / 0.28 (48496) hydrogen bonds : bond 0.03671 / 2.48 ( 1401) hydrogen bonds : angle 4.82374 / 3.49 ( 3990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9633 (t80) cc_final: 0.9223 (t80) REVERT: A 240 LYS cc_start: 0.9529 (mmtm) cc_final: 0.9198 (mmtt) REVERT: A 260 GLU cc_start: 0.8573 (mp0) cc_final: 0.8286 (tp30) REVERT: A 288 MET cc_start: 0.7784 (pmm) cc_final: 0.7113 (pmm) REVERT: B 89 MET cc_start: 0.8986 (ttt) cc_final: 0.8727 (ttm) REVERT: B 240 LYS cc_start: 0.9735 (mtmm) cc_final: 0.9261 (mmmm) REVERT: B 253 MET cc_start: 0.8455 (ppp) cc_final: 0.8060 (ppp) REVERT: B 264 CYS cc_start: 0.8511 (m) cc_final: 0.7951 (m) REVERT: B 288 MET cc_start: 0.8471 (pmm) cc_final: 0.7931 (pmm) REVERT: C 40 LYS cc_start: 0.8810 (tptp) cc_final: 0.8253 (ttpt) REVERT: C 213 MET cc_start: -0.1011 (mmt) cc_final: -0.1246 (mmt) REVERT: C 215 GLN cc_start: 0.7387 (tt0) cc_final: 0.6693 (tt0) REVERT: C 240 LYS cc_start: 0.9626 (mttt) cc_final: 0.9235 (mptt) REVERT: C 250 LEU cc_start: 0.9255 (pt) cc_final: 0.7702 (pt) REVERT: C 253 MET cc_start: 0.9194 (ttm) cc_final: 0.8409 (ttm) REVERT: C 310 TYR cc_start: 0.8894 (m-10) cc_final: 0.8544 (m-80) REVERT: D 186 MET cc_start: 0.8994 (mpp) cc_final: 0.8527 (mpp) REVERT: D 190 LEU cc_start: 0.9723 (mt) cc_final: 0.9314 (pp) REVERT: D 229 CYS cc_start: 0.9663 (m) cc_final: 0.9441 (m) REVERT: D 232 HIS cc_start: 0.9798 (t-90) cc_final: 0.9342 (t-90) REVERT: D 236 LYS cc_start: 0.9731 (ttmt) cc_final: 0.9528 (ttmt) REVERT: D 240 LYS cc_start: 0.9753 (mttt) cc_final: 0.9354 (mmmt) REVERT: D 250 LEU cc_start: 0.9594 (pp) cc_final: 0.8671 (pp) REVERT: D 253 MET cc_start: 0.8878 (ttm) cc_final: 0.8414 (ttm) REVERT: E 87 MET cc_start: 0.8045 (tpt) cc_final: 0.7772 (tpp) REVERT: E 232 HIS cc_start: 0.9782 (t-90) cc_final: 0.9502 (t-90) REVERT: E 253 MET cc_start: 0.9365 (ttm) cc_final: 0.8842 (ttm) REVERT: E 264 CYS cc_start: 0.9596 (t) cc_final: 0.9394 (t) REVERT: E 295 PHE cc_start: 0.9627 (t80) cc_final: 0.9396 (t80) REVERT: F 193 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9083 (mm) REVERT: F 197 MET cc_start: 0.9477 (mmt) cc_final: 0.9178 (mmm) REVERT: G 1 MET cc_start: -0.2460 (ttt) cc_final: -0.2731 (ttt) REVERT: G 77 MET cc_start: 0.7063 (ppp) cc_final: 0.6732 (ppp) REVERT: G 87 MET cc_start: 0.8901 (tpp) cc_final: 0.7337 (mmm) REVERT: G 89 MET cc_start: 0.9363 (ttm) cc_final: 0.9084 (ttt) REVERT: H 193 ILE cc_start: 0.9927 (OUTLIER) cc_final: 0.9718 (pt) REVERT: H 253 MET cc_start: 0.9228 (mmm) cc_final: 0.8970 (mmm) REVERT: H 295 PHE cc_start: 0.9662 (t80) cc_final: 0.9354 (t80) REVERT: H 303 LEU cc_start: 0.9477 (tt) cc_final: 0.9277 (mt) REVERT: I 58 CYS cc_start: 0.8868 (m) cc_final: 0.8003 (m) REVERT: I 89 MET cc_start: 0.9510 (mmp) cc_final: 0.9198 (mmp) REVERT: I 232 HIS cc_start: 0.9447 (t70) cc_final: 0.9153 (t-170) REVERT: I 236 LYS cc_start: 0.9793 (ttmm) cc_final: 0.9396 (ttmm) REVERT: I 288 MET cc_start: 0.7377 (ptp) cc_final: 0.6875 (ptm) REVERT: I 291 MET cc_start: 0.8922 (ptm) cc_final: 0.8251 (ppp) REVERT: I 306 PHE cc_start: 0.9272 (m-10) cc_final: 0.9037 (m-10) REVERT: J 197 MET cc_start: 0.9284 (mmm) cc_final: 0.8974 (mmm) REVERT: J 288 MET cc_start: 0.8370 (ptt) cc_final: 0.8126 (ptm) outliers start: 3 outliers final: 0 residues processed: 326 average time/residue: 0.2095 time to fit residues: 113.4421 Evaluate side-chains 254 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [184, 358, 421, 374, 373, 128, 109, 362, 179, 107, 34] chunk 184 optimal weight: 5.9990 chunk 358 optimal weight: 5.9990 chunk 421 optimal weight: 0.3980 chunk 374 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 362 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 34 optimal weight: 40.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS A 391 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.044137 restraints weight = 222136.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.045017 restraints weight = 186437.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045647 restraints weight = 165240.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046112 restraints weight = 150853.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046514 restraints weight = 141496.718| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35688 Z= 0.122 Angle : 0.508 6.821 48496 Z= 0.265 Chirality : 0.039 0.147 5380 Planarity : 0.003 0.044 6408 Dihedral : 4.068 22.432 5068 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.03 % Allowed : 1.25 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 4550 helix: 1.58 (0.12), residues: 1830 sheet: -0.59 (0.20), residues: 690 loop : 0.62 (0.15), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 456 TYR 0.015 0.001 TYR B 430 PHE 0.016 0.001 PHE H 292 TRP 0.019 0.001 TRP E 101 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (35688) covalent geometry : angle 0.50787 / 0.27 (48496) hydrogen bonds : bond 0.03488 / 2.35 ( 1401) hydrogen bonds : angle 4.73270 / 3.43 ( 3990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9477 (mmm) cc_final: 0.9203 (mmp) REVERT: A 235 TYR cc_start: 0.9643 (t80) cc_final: 0.9141 (t80) REVERT: A 240 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9196 (mmtt) REVERT: A 248 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9106 (mmmm) REVERT: A 264 CYS cc_start: 0.8828 (p) cc_final: 0.8549 (p) REVERT: A 288 MET cc_start: 0.7919 (pmm) cc_final: 0.7619 (pmm) REVERT: B 33 MET cc_start: 0.9564 (mpp) cc_final: 0.9161 (mmp) REVERT: B 89 MET cc_start: 0.9022 (ttt) cc_final: 0.8778 (ttt) REVERT: B 240 LYS cc_start: 0.9735 (mtmm) cc_final: 0.9269 (mmmm) REVERT: B 253 MET cc_start: 0.8261 (ppp) cc_final: 0.7945 (ppp) REVERT: C 40 LYS cc_start: 0.8916 (tptp) cc_final: 0.8276 (ttpt) REVERT: C 215 GLN cc_start: 0.7376 (tt0) cc_final: 0.6771 (tt0) REVERT: C 240 LYS cc_start: 0.9607 (mttt) cc_final: 0.9205 (mptt) REVERT: C 253 MET cc_start: 0.9190 (ttm) cc_final: 0.8411 (ttm) REVERT: C 310 TYR cc_start: 0.8899 (m-10) cc_final: 0.8536 (m-80) REVERT: D 186 MET cc_start: 0.9005 (mpp) cc_final: 0.8612 (mpp) REVERT: D 190 LEU cc_start: 0.9717 (mt) cc_final: 0.9292 (pp) REVERT: D 229 CYS cc_start: 0.9629 (m) cc_final: 0.9410 (m) REVERT: D 232 HIS cc_start: 0.9814 (t-90) cc_final: 0.9529 (t-90) REVERT: D 240 LYS cc_start: 0.9721 (mttt) cc_final: 0.9343 (mmmt) REVERT: D 250 LEU cc_start: 0.9584 (pp) cc_final: 0.8655 (pp) REVERT: D 253 MET cc_start: 0.8866 (ttm) cc_final: 0.8420 (ttm) REVERT: D 288 MET cc_start: 0.8490 (ptm) cc_final: 0.7938 (ptm) REVERT: E 87 MET cc_start: 0.8077 (tpt) cc_final: 0.7839 (tpp) REVERT: E 232 HIS cc_start: 0.9797 (t-90) cc_final: 0.9534 (t-90) REVERT: E 253 MET cc_start: 0.9259 (ttm) cc_final: 0.8764 (ttm) REVERT: E 255 LYS cc_start: 0.9107 (tppp) cc_final: 0.8904 (tppp) REVERT: E 264 CYS cc_start: 0.9538 (t) cc_final: 0.9316 (t) REVERT: E 295 PHE cc_start: 0.9625 (t80) cc_final: 0.9382 (t80) REVERT: F 197 MET cc_start: 0.9456 (mmt) cc_final: 0.9138 (mmm) REVERT: G 77 MET cc_start: 0.7090 (ppp) cc_final: 0.6829 (ppp) REVERT: G 87 MET cc_start: 0.8838 (tpp) cc_final: 0.7443 (mmm) REVERT: G 197 MET cc_start: 0.9414 (mmm) cc_final: 0.9161 (mmt) REVERT: H 253 MET cc_start: 0.9177 (mmm) cc_final: 0.8944 (mmm) REVERT: H 295 PHE cc_start: 0.9696 (t80) cc_final: 0.9375 (t80) REVERT: H 448 TRP cc_start: 0.9656 (t-100) cc_final: 0.9414 (t-100) REVERT: I 58 CYS cc_start: 0.8880 (m) cc_final: 0.7993 (m) REVERT: I 89 MET cc_start: 0.9542 (mmp) cc_final: 0.9214 (mmp) REVERT: I 232 HIS cc_start: 0.9460 (t70) cc_final: 0.9185 (t-170) REVERT: I 236 LYS cc_start: 0.9787 (ttmm) cc_final: 0.9078 (mmmm) REVERT: I 240 LYS cc_start: 0.9684 (mptt) cc_final: 0.9194 (mmtt) REVERT: I 288 MET cc_start: 0.7435 (ptp) cc_final: 0.6912 (ptm) REVERT: I 291 MET cc_start: 0.8897 (ptm) cc_final: 0.8233 (ppp) REVERT: I 306 PHE cc_start: 0.9266 (m-10) cc_final: 0.8903 (m-80) REVERT: J 77 MET cc_start: 0.5892 (tmm) cc_final: 0.5018 (ppp) REVERT: J 288 MET cc_start: 0.8321 (ptt) cc_final: 0.8091 (ptm) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.2115 time to fit residues: 112.4884 Evaluate side-chains 253 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [264, 57, 221, 304, 444, 71, 157, 187, 287, 351, 192] chunk 264 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 444 optimal weight: 0.0770 chunk 71 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 187 optimal weight: 40.0000 chunk 287 optimal weight: 0.9990 chunk 351 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.064174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044290 restraints weight = 234017.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.045208 restraints weight = 193772.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045880 restraints weight = 170644.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.046388 restraints weight = 155874.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.046690 restraints weight = 145981.470| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35688 Z= 0.103 Angle : 0.493 7.589 48496 Z= 0.257 Chirality : 0.039 0.140 5380 Planarity : 0.003 0.041 6408 Dihedral : 3.961 21.525 5068 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4550 helix: 1.68 (0.12), residues: 1830 sheet: -0.31 (0.19), residues: 790 loop : 0.74 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 158 TYR 0.013 0.001 TYR A 376 PHE 0.016 0.001 PHE I 295 TRP 0.015 0.001 TRP F 80 HIS 0.004 0.001 HIS F 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (35688) covalent geometry : angle 0.49342 / 0.26 (48496) hydrogen bonds : bond 0.03381 / 2.27 ( 1401) hydrogen bonds : angle 4.65889 / 3.38 ( 3990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9161 (mmm) cc_final: 0.8940 (mmm) REVERT: A 197 MET cc_start: 0.9569 (mmm) cc_final: 0.9140 (mmp) REVERT: A 235 TYR cc_start: 0.9628 (t80) cc_final: 0.9149 (t80) REVERT: A 240 LYS cc_start: 0.9523 (mmtm) cc_final: 0.9189 (mmtt) REVERT: A 248 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9130 (mmmm) REVERT: A 264 CYS cc_start: 0.8715 (p) cc_final: 0.8446 (p) REVERT: A 288 MET cc_start: 0.7974 (pmm) cc_final: 0.7474 (pmm) REVERT: B 33 MET cc_start: 0.9571 (mpp) cc_final: 0.9149 (mmp) REVERT: B 89 MET cc_start: 0.9063 (ttt) cc_final: 0.8785 (ttt) REVERT: B 253 MET cc_start: 0.8293 (ppp) cc_final: 0.7772 (ppp) REVERT: C 40 LYS cc_start: 0.8929 (tptp) cc_final: 0.8370 (ttpt) REVERT: C 215 GLN cc_start: 0.7224 (tt0) cc_final: 0.6598 (tt0) REVERT: C 232 HIS cc_start: 0.9793 (t-90) cc_final: 0.9177 (t-90) REVERT: C 253 MET cc_start: 0.9221 (ttm) cc_final: 0.8427 (ttm) REVERT: C 288 MET cc_start: 0.8916 (ptm) cc_final: 0.8694 (ptm) REVERT: D 186 MET cc_start: 0.8996 (mpp) cc_final: 0.8592 (mpp) REVERT: D 190 LEU cc_start: 0.9713 (mt) cc_final: 0.9283 (pp) REVERT: D 232 HIS cc_start: 0.9801 (t-90) cc_final: 0.9438 (t-90) REVERT: D 240 LYS cc_start: 0.9731 (mttt) cc_final: 0.9370 (mmmt) REVERT: D 250 LEU cc_start: 0.9558 (pp) cc_final: 0.8815 (pp) REVERT: D 253 MET cc_start: 0.8750 (ttm) cc_final: 0.8354 (ttm) REVERT: D 288 MET cc_start: 0.8569 (ptm) cc_final: 0.7864 (ptm) REVERT: D 437 GLU cc_start: 0.9636 (mp0) cc_final: 0.9408 (mp0) REVERT: E 87 MET cc_start: 0.8297 (tpt) cc_final: 0.8067 (tpp) REVERT: E 232 HIS cc_start: 0.9795 (t-90) cc_final: 0.9508 (t-90) REVERT: E 253 MET cc_start: 0.9203 (ttm) cc_final: 0.8769 (ttm) REVERT: E 295 PHE cc_start: 0.9620 (t80) cc_final: 0.9370 (t80) REVERT: F 197 MET cc_start: 0.9450 (mmt) cc_final: 0.9092 (mmm) REVERT: F 253 MET cc_start: 0.8380 (mmt) cc_final: 0.8039 (mmt) REVERT: G 1 MET cc_start: -0.2081 (ttt) cc_final: -0.2304 (ttt) REVERT: G 77 MET cc_start: 0.7102 (ppp) cc_final: 0.6822 (ppp) REVERT: G 87 MET cc_start: 0.8889 (tpp) cc_final: 0.7215 (mmm) REVERT: H 1 MET cc_start: 0.2831 (tpt) cc_final: 0.2517 (tpt) REVERT: H 89 MET cc_start: 0.9126 (ptp) cc_final: 0.8878 (ppp) REVERT: H 253 MET cc_start: 0.9150 (mmm) cc_final: 0.8905 (mmm) REVERT: H 295 PHE cc_start: 0.9710 (t80) cc_final: 0.9431 (t80) REVERT: I 58 CYS cc_start: 0.8918 (m) cc_final: 0.8022 (m) REVERT: I 89 MET cc_start: 0.9541 (mmp) cc_final: 0.9212 (mmp) REVERT: I 232 HIS cc_start: 0.9441 (t70) cc_final: 0.9142 (t-170) REVERT: I 236 LYS cc_start: 0.9775 (ttmm) cc_final: 0.9119 (mmmm) REVERT: I 240 LYS cc_start: 0.9696 (mptt) cc_final: 0.9124 (mmtt) REVERT: I 288 MET cc_start: 0.7440 (ptp) cc_final: 0.6941 (ptm) REVERT: I 291 MET cc_start: 0.8947 (ptm) cc_final: 0.8280 (ppp) REVERT: J 77 MET cc_start: 0.5491 (tmm) cc_final: 0.4528 (ppp) REVERT: J 288 MET cc_start: 0.8347 (ptt) cc_final: 0.8090 (ptm) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2070 time to fit residues: 109.4533 Evaluate side-chains 258 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [106, 129, 55, 359, 61, 42, 69, 285, 338, 243, 448] chunk 106 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 chunk 55 optimal weight: 0.0980 chunk 359 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 338 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 246 HIS F 286 HIS ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN I 232 HIS ** J 232 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 = 0.3500 r_free = 0.3500 target = 0.063734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.044249 restraints weight = 243485.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045242 restraints weight = 200881.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045957 restraints weight = 175585.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046487 restraints weight = 159680.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046849 restraints weight = 149321.049| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35688 Z= 0.144 Angle : 0.525 7.279 48496 Z= 0.275 Chirality : 0.039 0.147 5380 Planarity : 0.003 0.053 6408 Dihedral : 4.019 21.327 5068 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.03 % Allowed : 0.81 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.13), residues: 4550 helix: 1.64 (0.12), residues: 1830 sheet: -0.55 (0.20), residues: 690 loop : 0.59 (0.15), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 166 TYR 0.016 0.001 TYR B 430 PHE 0.020 0.001 PHE D 292 TRP 0.029 0.001 TRP E 101 HIS 0.007 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (35688) covalent geometry : angle 0.52500 / 0.27 (48496) hydrogen bonds : bond 0.03424 / 2.30 ( 1401) hydrogen bonds : angle 4.73056 / 3.43 ( 3990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6718 (mmp) cc_final: 0.6416 (mmp) REVERT: A 197 MET cc_start: 0.9604 (mmm) cc_final: 0.9246 (mmp) REVERT: A 235 TYR cc_start: 0.9619 (t80) cc_final: 0.9157 (t80) REVERT: A 240 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9238 (mmtt) REVERT: A 248 LYS cc_start: 0.9542 (mmtm) cc_final: 0.9151 (mmmm) REVERT: A 288 MET cc_start: 0.7979 (pmm) cc_final: 0.7408 (pmm) REVERT: A 291 MET cc_start: 0.8424 (ppp) cc_final: 0.8139 (ppp) REVERT: B 33 MET cc_start: 0.9636 (mpp) cc_final: 0.9264 (mmp) REVERT: B 89 MET cc_start: 0.9123 (ttt) cc_final: 0.8870 (ttt) REVERT: B 253 MET cc_start: 0.8377 (ppp) cc_final: 0.7861 (ppp) REVERT: C 40 LYS cc_start: 0.8978 (tptp) cc_final: 0.8463 (ttpt) REVERT: C 213 MET cc_start: -0.0699 (mmp) cc_final: -0.0917 (mmp) REVERT: C 215 GLN cc_start: 0.7261 (tt0) cc_final: 0.6702 (tt0) REVERT: C 240 LYS cc_start: 0.9627 (mttt) cc_final: 0.9242 (mptt) REVERT: C 253 MET cc_start: 0.9273 (ttm) cc_final: 0.8436 (ttm) REVERT: C 288 MET cc_start: 0.9042 (ptm) cc_final: 0.8691 (ttp) REVERT: D 77 MET cc_start: 0.7191 (mmp) cc_final: 0.6320 (pmm) REVERT: D 183 SER cc_start: 0.9524 (m) cc_final: 0.9318 (p) REVERT: D 186 MET cc_start: 0.9109 (mpp) cc_final: 0.8703 (mpp) REVERT: D 190 LEU cc_start: 0.9729 (mt) cc_final: 0.9287 (pp) REVERT: D 232 HIS cc_start: 0.9806 (t-90) cc_final: 0.9530 (t-90) REVERT: D 240 LYS cc_start: 0.9719 (mttt) cc_final: 0.9384 (mmmt) REVERT: D 253 MET cc_start: 0.8773 (ttm) cc_final: 0.8288 (ttm) REVERT: D 437 GLU cc_start: 0.9645 (mp0) cc_final: 0.9346 (mp0) REVERT: E 87 MET cc_start: 0.8435 (tpt) cc_final: 0.8143 (tpp) REVERT: E 232 HIS cc_start: 0.9820 (t-90) cc_final: 0.9525 (t-90) REVERT: E 236 LYS cc_start: 0.9825 (ttmm) cc_final: 0.9607 (tttt) REVERT: E 253 MET cc_start: 0.9211 (ttm) cc_final: 0.8708 (ttm) REVERT: E 295 PHE cc_start: 0.9610 (t80) cc_final: 0.9372 (t80) REVERT: F 197 MET cc_start: 0.9471 (mmt) cc_final: 0.9176 (mmm) REVERT: F 213 MET cc_start: -0.5469 (ppp) cc_final: -0.5968 (ppp) REVERT: F 253 MET cc_start: 0.8522 (mmt) cc_final: 0.8187 (mmt) REVERT: G 1 MET cc_start: -0.1868 (ttt) cc_final: -0.2086 (ttt) REVERT: G 77 MET cc_start: 0.7201 (ppp) cc_final: 0.6881 (ppp) REVERT: G 87 MET cc_start: 0.8870 (tpp) cc_final: 0.8165 (mmm) REVERT: G 197 MET cc_start: 0.9554 (mmm) cc_final: 0.8954 (mmt) REVERT: H 89 MET cc_start: 0.9188 (ptp) cc_final: 0.8963 (ppp) REVERT: H 253 MET cc_start: 0.9116 (mmm) cc_final: 0.8842 (mmm) REVERT: H 295 PHE cc_start: 0.9704 (t80) cc_final: 0.9383 (t80) REVERT: I 58 CYS cc_start: 0.8847 (m) cc_final: 0.7926 (m) REVERT: I 89 MET cc_start: 0.9542 (mmp) cc_final: 0.9240 (mmp) REVERT: I 232 HIS cc_start: 0.9390 (t-90) cc_final: 0.9095 (t-170) REVERT: I 236 LYS cc_start: 0.9784 (ttmm) cc_final: 0.9057 (mmmm) REVERT: I 240 LYS cc_start: 0.9707 (mptt) cc_final: 0.9179 (mmtt) REVERT: I 288 MET cc_start: 0.7632 (ptp) cc_final: 0.7161 (ptm) REVERT: I 291 MET cc_start: 0.8979 (ptm) cc_final: 0.8318 (ppp) REVERT: J 197 MET cc_start: 0.9585 (mmt) cc_final: 0.9116 (mmm) REVERT: J 253 MET cc_start: 0.8928 (ptp) cc_final: 0.8723 (ptp) REVERT: J 288 MET cc_start: 0.8377 (ptt) cc_final: 0.8141 (ptm) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.2061 time to fit residues: 107.9470 Evaluate side-chains 246 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [377, 421, 251, 167, 444, 208, 445, 419, 327, 254, 332] chunk 377 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 444 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 chunk 445 optimal weight: 6.9990 chunk 419 optimal weight: 20.0000 chunk 327 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS A 299 GLN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.044536 restraints weight = 240567.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.045496 restraints weight = 198301.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.046197 restraints weight = 173972.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.046726 restraints weight = 158711.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047098 restraints weight = 148455.936| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 35688 Z= 0.112 Angle : 0.505 9.557 48496 Z= 0.263 Chirality : 0.039 0.136 5380 Planarity : 0.003 0.055 6408 Dihedral : 3.918 21.134 5068 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.13), residues: 4550 helix: 1.66 (0.12), residues: 1830 sheet: -0.38 (0.19), residues: 770 loop : 0.70 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.020 0.001 TYR E 235 PHE 0.017 0.001 PHE I 295 TRP 0.018 0.001 TRP E 101 HIS 0.006 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (35688) covalent geometry : angle 0.50458 / 0.26 (48496) hydrogen bonds : bond 0.03364 / 2.26 ( 1401) hydrogen bonds : angle 4.69713 / 3.41 ( 3990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9600 (mmm) cc_final: 0.9187 (mmp) REVERT: A 213 MET cc_start: -0.2422 (tmm) cc_final: -0.3842 (ppp) REVERT: A 235 TYR cc_start: 0.9596 (t80) cc_final: 0.9142 (t80) REVERT: A 240 LYS cc_start: 0.9468 (mmtm) cc_final: 0.9231 (mmtt) REVERT: A 264 CYS cc_start: 0.9417 (t) cc_final: 0.8561 (p) REVERT: A 288 MET cc_start: 0.7951 (pmm) cc_final: 0.7344 (pmm) REVERT: B 33 MET cc_start: 0.9614 (mpp) cc_final: 0.9235 (mmp) REVERT: B 89 MET cc_start: 0.9097 (ttt) cc_final: 0.8829 (ttt) REVERT: B 253 MET cc_start: 0.8327 (ppp) cc_final: 0.7776 (ppp) REVERT: C 40 LYS cc_start: 0.9003 (tptp) cc_final: 0.8582 (ttpt) REVERT: C 213 MET cc_start: -0.0500 (mmp) cc_final: -0.0726 (mmt) REVERT: C 215 GLN cc_start: 0.7178 (tt0) cc_final: 0.6700 (tt0) REVERT: C 232 HIS cc_start: 0.9798 (t-90) cc_final: 0.9253 (t-90) REVERT: C 253 MET cc_start: 0.9241 (ttm) cc_final: 0.8446 (ttm) REVERT: C 288 MET cc_start: 0.9072 (ptm) cc_final: 0.8669 (ttp) REVERT: D 77 MET cc_start: 0.7197 (mmp) cc_final: 0.6286 (pmm) REVERT: D 149 GLU cc_start: 0.8119 (pt0) cc_final: 0.7719 (pt0) REVERT: D 186 MET cc_start: 0.9002 (mpp) cc_final: 0.8771 (mpp) REVERT: D 232 HIS cc_start: 0.9770 (t-90) cc_final: 0.9530 (t-90) REVERT: D 240 LYS cc_start: 0.9711 (mttt) cc_final: 0.9360 (mmmt) REVERT: D 250 LEU cc_start: 0.9593 (pp) cc_final: 0.8725 (pp) REVERT: D 253 MET cc_start: 0.8839 (ttm) cc_final: 0.8319 (ttm) REVERT: D 310 TYR cc_start: 0.9307 (m-10) cc_final: 0.9026 (m-10) REVERT: D 437 GLU cc_start: 0.9647 (mp0) cc_final: 0.9364 (mp0) REVERT: E 87 MET cc_start: 0.8432 (tpt) cc_final: 0.8176 (tpp) REVERT: E 232 HIS cc_start: 0.9784 (t-90) cc_final: 0.9546 (t-90) REVERT: E 235 TYR cc_start: 0.9732 (t80) cc_final: 0.9487 (t80) REVERT: E 253 MET cc_start: 0.9138 (ttm) cc_final: 0.8698 (ttm) REVERT: E 255 LYS cc_start: 0.9074 (tppp) cc_final: 0.8510 (tppp) REVERT: E 295 PHE cc_start: 0.9611 (t80) cc_final: 0.9361 (t80) REVERT: F 197 MET cc_start: 0.9437 (mmt) cc_final: 0.9111 (mmm) REVERT: F 253 MET cc_start: 0.8556 (mmt) cc_final: 0.8181 (mmt) REVERT: G 1 MET cc_start: -0.1806 (ttt) cc_final: -0.2014 (ttt) REVERT: G 77 MET cc_start: 0.7217 (ppp) cc_final: 0.6860 (ppp) REVERT: G 87 MET cc_start: 0.8872 (tpp) cc_final: 0.8168 (mmm) REVERT: G 197 MET cc_start: 0.9524 (mmm) cc_final: 0.8972 (mmt) REVERT: H 1 MET cc_start: 0.4028 (tpt) cc_final: 0.3798 (tpt) REVERT: H 87 MET cc_start: 0.8037 (tpp) cc_final: 0.7759 (tpp) REVERT: H 253 MET cc_start: 0.9128 (mmm) cc_final: 0.8875 (mmm) REVERT: H 295 PHE cc_start: 0.9703 (t80) cc_final: 0.9386 (t80) REVERT: I 58 CYS cc_start: 0.8849 (m) cc_final: 0.7923 (m) REVERT: I 89 MET cc_start: 0.9542 (mmp) cc_final: 0.9245 (mmp) REVERT: I 232 HIS cc_start: 0.9487 (t-90) cc_final: 0.9026 (t-170) REVERT: I 236 LYS cc_start: 0.9788 (ttmm) cc_final: 0.8972 (mmmm) REVERT: I 240 LYS cc_start: 0.9711 (mptt) cc_final: 0.9134 (mmtt) REVERT: I 288 MET cc_start: 0.7651 (ptp) cc_final: 0.7171 (ptm) REVERT: I 291 MET cc_start: 0.9009 (ptm) cc_final: 0.8339 (ppp) REVERT: J 288 MET cc_start: 0.8373 (ptt) cc_final: 0.8112 (ptm) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.2066 time to fit residues: 109.7408 Evaluate side-chains 255 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [324, 343, 423, 60, 374, 172, 398, 238, 432, 333, 268] chunk 324 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 423 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 398 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.061879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042769 restraints weight = 253893.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043680 restraints weight = 211096.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044339 restraints weight = 185128.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.044817 restraints weight = 169467.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045148 restraints weight = 159077.059| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 35688 Z= 0.209 Angle : 0.609 10.414 48496 Z= 0.320 Chirality : 0.041 0.143 5380 Planarity : 0.004 0.049 6408 Dihedral : 4.269 21.542 5068 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4550 helix: 1.38 (0.12), residues: 1820 sheet: -0.67 (0.19), residues: 740 loop : 0.49 (0.15), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 319 TYR 0.022 0.002 TYR B 430 PHE 0.020 0.002 PHE G 292 TRP 0.035 0.002 TRP E 101 HIS 0.009 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (35688) covalent geometry : angle 0.60907 / 0.32 (48496) hydrogen bonds : bond 0.03665 / 2.45 ( 1401) hydrogen bonds : angle 4.93724 / 3.57 ( 3990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9638 (mmm) cc_final: 0.9207 (mmp) REVERT: A 213 MET cc_start: -0.1978 (tmm) cc_final: -0.3551 (ppp) REVERT: A 235 TYR cc_start: 0.9608 (t80) cc_final: 0.9073 (t80) REVERT: A 240 LYS cc_start: 0.9533 (mmtm) cc_final: 0.9314 (mmtt) REVERT: A 264 CYS cc_start: 0.9376 (t) cc_final: 0.8625 (p) REVERT: A 288 MET cc_start: 0.8021 (pmm) cc_final: 0.7304 (pmm) REVERT: B 33 MET cc_start: 0.9687 (mpp) cc_final: 0.9375 (mmp) REVERT: B 89 MET cc_start: 0.9164 (ttt) cc_final: 0.8944 (ttt) REVERT: B 253 MET cc_start: 0.8509 (ppp) cc_final: 0.8035 (ppp) REVERT: C 40 LYS cc_start: 0.9065 (tptp) cc_final: 0.8643 (mtmt) REVERT: C 215 GLN cc_start: 0.7341 (tt0) cc_final: 0.7058 (tt0) REVERT: C 240 LYS cc_start: 0.9658 (mttt) cc_final: 0.9276 (mptt) REVERT: C 253 MET cc_start: 0.9215 (ttm) cc_final: 0.8433 (ttm) REVERT: D 186 MET cc_start: 0.9028 (mpp) cc_final: 0.8641 (mpp) REVERT: D 190 LEU cc_start: 0.9714 (mt) cc_final: 0.9281 (pp) REVERT: D 232 HIS cc_start: 0.9804 (t-90) cc_final: 0.9494 (t-90) REVERT: D 240 LYS cc_start: 0.9726 (mttt) cc_final: 0.9386 (mmmt) REVERT: D 253 MET cc_start: 0.8823 (ttm) cc_final: 0.8290 (ttm) REVERT: E 87 MET cc_start: 0.8646 (tpt) cc_final: 0.8394 (tpp) REVERT: E 232 HIS cc_start: 0.9818 (t-90) cc_final: 0.9467 (t-90) REVERT: E 253 MET cc_start: 0.9231 (ttm) cc_final: 0.8633 (ttm) REVERT: E 255 LYS cc_start: 0.9130 (tppp) cc_final: 0.8583 (tppp) REVERT: F 87 MET cc_start: 0.7179 (mmm) cc_final: 0.6326 (mmm) REVERT: F 197 MET cc_start: 0.9520 (mmt) cc_final: 0.9141 (mmm) REVERT: F 213 MET cc_start: -0.5252 (ppp) cc_final: -0.5708 (ppp) REVERT: F 253 MET cc_start: 0.8628 (mmt) cc_final: 0.8281 (mmt) REVERT: G 87 MET cc_start: 0.8877 (tpp) cc_final: 0.8396 (mmm) REVERT: G 197 MET cc_start: 0.9548 (mmm) cc_final: 0.8815 (tmm) REVERT: H 1 MET cc_start: 0.4591 (tpt) cc_final: 0.4369 (tpt) REVERT: H 253 MET cc_start: 0.9123 (mmm) cc_final: 0.8884 (mmm) REVERT: H 295 PHE cc_start: 0.9721 (t80) cc_final: 0.9490 (t80) REVERT: I 197 MET cc_start: 0.9793 (mmm) cc_final: 0.9450 (mmm) REVERT: I 213 MET cc_start: -0.0941 (tmm) cc_final: -0.1981 (ttp) REVERT: I 232 HIS cc_start: 0.9551 (t-90) cc_final: 0.9084 (t-170) REVERT: I 236 LYS cc_start: 0.9782 (ttmm) cc_final: 0.9151 (ttmm) REVERT: I 240 LYS cc_start: 0.9750 (mptt) cc_final: 0.9201 (mmtt) REVERT: I 288 MET cc_start: 0.7780 (ptp) cc_final: 0.7434 (ptm) REVERT: I 291 MET cc_start: 0.9044 (ptm) cc_final: 0.8418 (ppp) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2145 time to fit residues: 105.6174 Evaluate side-chains 229 residues out of total 3590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [33, 297, 9, 248, 429, 78, 112, 403, 67, 85, 76] chunk 33 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 429 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 383 GLN J 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043432 restraints weight = 243013.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044365 restraints weight = 200837.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045020 restraints weight = 176072.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045497 restraints weight = 160882.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045848 restraints weight = 151357.905| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35688 Z= 0.118 Angle : 0.527 9.148 48496 Z= 0.274 Chirality : 0.040 0.138 5380 Planarity : 0.003 0.041 6408 Dihedral : 4.082 21.126 5068 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4550 helix: 1.50 (0.12), residues: 1830 sheet: -0.69 (0.21), residues: 670 loop : 0.48 (0.15), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.014 0.001 TYR B 430 PHE 0.018 0.001 PHE G 292 TRP 0.030 0.001 TRP E 448 HIS 0.011 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (35688) covalent geometry : angle 0.52739 / 0.27 (48496) hydrogen bonds : bond 0.03457 / 2.31 ( 1401) hydrogen bonds : angle 4.77700 / 3.46 ( 3990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5376.72 seconds wall clock time: 93 minutes 57.48 seconds (5637.48 seconds total)