Starting phenix.real_space_refine on Sat Feb 7 06:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.map" model { file = "/net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m67_63660/02_2026/9m67_63660.cif" } resolution = 3.4 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= -0.000 sd= 0.011 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 25 5.16 5 C 18730 2.51 5 N 5280 2.21 5 O 6605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30640 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3147 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 415} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2981 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 4, 'TRANS': 404} Chain: "C" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3147 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 415} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2981 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 4, 'TRANS': 404} Chain: "E" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3147 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 415} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2981 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 4, 'TRANS': 404} Chain: "G" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3147 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 415} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2981 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 4, 'TRANS': 404} Chain: "I" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3147 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 415} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2981 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 4, 'TRANS': 404} Time building chain proxies: 6.64, per 1000 atoms: 0.22 Number of scatterers: 30640 At special positions: 0 Unit cell: (205.96, 206.72, 133.76, 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 25 16.00 O 6605 8.00 N 5280 7.00 C 18730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7650 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 46 sheets defined 41.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 20 through 65 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.724A pdb=" N LEU A 69 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.857A pdb=" N ASP A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 269 through 294 Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.995A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 385 through 399 Processing helix chain 'A' and resid 402 through 440 Processing helix chain 'B' and resid 47 through 101 Processing helix chain 'B' and resid 105 through 128 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 407 through 454 Processing helix chain 'C' and resid 21 through 65 Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.684A pdb=" N LEU C 69 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.922A pdb=" N ASP C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 269 through 294 Processing helix chain 'C' and resid 315 through 328 removed outlier: 4.009A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 402 through 440 removed outlier: 3.530A pdb=" N PHE C 440 " --> pdb=" O TYR C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 101 removed outlier: 3.522A pdb=" N ASN D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 289 through 300 Processing helix chain 'D' and resid 407 through 454 Processing helix chain 'E' and resid 21 through 65 Proline residue: E 32 - end of helix Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.725A pdb=" N LEU E 69 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.877A pdb=" N ASP E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 207 Processing helix chain 'E' and resid 269 through 294 Processing helix chain 'E' and resid 315 through 328 removed outlier: 3.986A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN E 328 " --> pdb=" O GLY E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 402 through 440 Processing helix chain 'F' and resid 47 through 101 Processing helix chain 'F' and resid 105 through 128 Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 289 through 300 Processing helix chain 'F' and resid 407 through 454 Processing helix chain 'G' and resid 21 through 65 Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.691A pdb=" N LEU G 69 " --> pdb=" O LYS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 removed outlier: 3.860A pdb=" N ASP G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 207 Processing helix chain 'G' and resid 269 through 294 Processing helix chain 'G' and resid 315 through 328 removed outlier: 4.031A pdb=" N ARG G 319 " --> pdb=" O ASP G 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN G 328 " --> pdb=" O GLY G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 344 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'G' and resid 369 through 378 Processing helix chain 'G' and resid 385 through 399 Processing helix chain 'G' and resid 402 through 440 Processing helix chain 'H' and resid 47 through 101 Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 169 through 173 Processing helix chain 'H' and resid 199 through 209 Processing helix chain 'H' and resid 289 through 300 Processing helix chain 'H' and resid 407 through 454 Processing helix chain 'I' and resid 21 through 65 Proline residue: I 32 - end of helix Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.726A pdb=" N LEU I 69 " --> pdb=" O LYS I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 removed outlier: 3.875A pdb=" N ASP I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 207 Processing helix chain 'I' and resid 269 through 294 Processing helix chain 'I' and resid 315 through 328 removed outlier: 4.079A pdb=" N ARG I 319 " --> pdb=" O ASP I 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN I 328 " --> pdb=" O GLY I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'I' and resid 369 through 378 Processing helix chain 'I' and resid 385 through 399 Processing helix chain 'I' and resid 402 through 440 Processing helix chain 'J' and resid 47 through 101 removed outlier: 3.542A pdb=" N ASN J 101 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 128 Processing helix chain 'J' and resid 169 through 173 removed outlier: 3.554A pdb=" N THR J 172 " --> pdb=" O GLY J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 289 through 300 Processing helix chain 'J' and resid 407 through 454 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 4.552A pdb=" N SER A 72 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 175 removed outlier: 7.295A pdb=" N GLU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU A 181 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN A 106 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER A 107 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 3.546A pdb=" N GLU A 134 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.816A pdb=" N SER B 249 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA9, first strand: chain 'B' and resid 347 through 351 removed outlier: 6.017A pdb=" N LEU B 361 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER B 375 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 371 " --> pdb=" O GLY B 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.538A pdb=" N SER C 72 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 175 removed outlier: 7.302A pdb=" N GLU C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU C 181 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN C 106 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 107 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 142 through 146 removed outlier: 3.551A pdb=" N GLU C 134 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 346 through 348 Processing sheet with id=AB6, first strand: chain 'D' and resid 180 through 184 Processing sheet with id=AB7, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.787A pdb=" N SER D 249 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'D' and resid 347 through 351 removed outlier: 6.463A pdb=" N LEU D 361 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER D 375 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 371 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 72 through 77 removed outlier: 4.553A pdb=" N SER E 72 " --> pdb=" O ASP E 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 83 through 86 Processing sheet with id=AC3, first strand: chain 'E' and resid 168 through 175 removed outlier: 7.305A pdb=" N GLU E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU E 181 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN E 106 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER E 107 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 142 through 146 removed outlier: 3.573A pdb=" N GLU E 134 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 346 through 348 Processing sheet with id=AC6, first strand: chain 'F' and resid 180 through 185 Processing sheet with id=AC7, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.734A pdb=" N SER F 249 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 335 through 337 Processing sheet with id=AC9, first strand: chain 'F' and resid 347 through 351 removed outlier: 6.547A pdb=" N LEU F 361 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER F 375 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR F 371 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 72 through 77 removed outlier: 4.579A pdb=" N SER G 72 " --> pdb=" O ASP G 268 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 83 through 86 Processing sheet with id=AD3, first strand: chain 'G' and resid 168 through 175 removed outlier: 7.301A pdb=" N GLU G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 181 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLN G 106 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER G 107 " --> pdb=" O LEU G 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.573A pdb=" N GLU G 134 " --> pdb=" O LYS G 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 346 through 348 Processing sheet with id=AD6, first strand: chain 'H' and resid 180 through 184 Processing sheet with id=AD7, first strand: chain 'H' and resid 230 through 232 removed outlier: 3.841A pdb=" N SER H 249 " --> pdb=" O THR H 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 335 through 337 Processing sheet with id=AD9, first strand: chain 'H' and resid 347 through 351 removed outlier: 6.535A pdb=" N LEU H 361 " --> pdb=" O SER H 375 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER H 375 " --> pdb=" O LEU H 361 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR H 371 " --> pdb=" O GLY H 365 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 72 through 77 removed outlier: 4.559A pdb=" N SER I 72 " --> pdb=" O ASP I 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=AE3, first strand: chain 'I' and resid 168 through 175 removed outlier: 7.294A pdb=" N GLU I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU I 181 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLN I 106 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER I 107 " --> pdb=" O LEU I 221 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 142 through 146 removed outlier: 3.593A pdb=" N GLU I 134 " --> pdb=" O LYS I 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 346 through 348 Processing sheet with id=AE6, first strand: chain 'J' and resid 180 through 184 Processing sheet with id=AE7, first strand: chain 'J' and resid 231 through 232 Processing sheet with id=AE8, first strand: chain 'J' and resid 249 through 250 removed outlier: 3.813A pdb=" N SER J 249 " --> pdb=" O THR J 258 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 335 through 337 Processing sheet with id=AF1, first strand: chain 'J' and resid 347 through 351 removed outlier: 5.799A pdb=" N LEU J 361 " --> pdb=" O SER J 375 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER J 375 " --> pdb=" O LEU J 361 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR J 371 " --> pdb=" O GLY J 365 " (cutoff:3.500A) 1775 hydrogen bonds defined for protein. 5046 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: 5.58 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10381 1.34 - 1.45: 2604 1.45 - 1.57: 17820 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 30855 Sorted by residual: bond pdb=" CB PRO A 32 " pdb=" CG PRO A 32 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO C 247 " pdb=" CG PRO C 247 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" CB PRO G 247 " pdb=" CG PRO G 247 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.41e+00 bond pdb=" CG LYS J 411 " pdb=" CD LYS J 411 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG LEU B 221 " pdb=" CD1 LEU B 221 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 30850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 40958 1.45 - 2.89: 720 2.89 - 4.34: 103 4.34 - 5.78: 33 5.78 - 7.23: 11 Bond angle restraints: 41825 Sorted by residual: angle pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" CD PRO A 32 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C PRO A 247 " pdb=" N GLN A 248 " pdb=" CA GLN A 248 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.49e+00 angle pdb=" C PRO E 247 " pdb=" N GLN E 248 " pdb=" CA GLN E 248 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.19e+00 angle pdb=" CA GLY G 188 " pdb=" C GLY G 188 " pdb=" O GLY G 188 " ideal model delta sigma weight residual 122.22 120.37 1.85 6.50e-01 2.37e+00 8.11e+00 angle pdb=" C PRO I 247 " pdb=" N GLN I 248 " pdb=" CA GLN I 248 " ideal model delta sigma weight residual 121.54 126.92 -5.38 1.91e+00 2.74e-01 7.94e+00 ... (remaining 41820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17396 17.94 - 35.87: 1265 35.87 - 53.81: 157 53.81 - 71.74: 33 71.74 - 89.68: 24 Dihedral angle restraints: 18875 sinusoidal: 6990 harmonic: 11885 Sorted by residual: dihedral pdb=" CA MET F 310 " pdb=" C MET F 310 " pdb=" N SER F 311 " pdb=" CA SER F 311 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LYS J 385 " pdb=" C LYS J 385 " pdb=" N ALA J 386 " pdb=" CA ALA J 386 " ideal model delta harmonic sigma weight residual 180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS H 178 " pdb=" C LYS H 178 " pdb=" N TYR H 179 " pdb=" CA TYR H 179 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 18872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3818 0.037 - 0.074: 995 0.074 - 0.111: 278 0.111 - 0.148: 89 0.148 - 0.185: 10 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CG LEU F 95 " pdb=" CB LEU F 95 " pdb=" CD1 LEU F 95 " pdb=" CD2 LEU F 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB ILE H 163 " pdb=" CA ILE H 163 " pdb=" CG1 ILE H 163 " pdb=" CG2 ILE H 163 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 5187 not shown) Planarity restraints: 5460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 31 " 0.066 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO A 32 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 31 " -0.051 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO G 32 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 246 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO I 247 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 247 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 247 " -0.030 5.00e-02 4.00e+02 ... (remaining 5457 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 735 2.70 - 3.25: 32070 3.25 - 3.80: 47727 3.80 - 4.35: 62155 4.35 - 4.90: 101874 Nonbonded interactions: 244561 Sorted by model distance: nonbonded pdb=" O LEU I 30 " pdb=" N THR I 34 " model vdw 2.147 3.120 nonbonded pdb=" O LEU A 30 " pdb=" N THR A 34 " model vdw 2.161 3.120 nonbonded pdb=" O GLY F 128 " pdb=" NZ LYS F 136 " model vdw 2.175 3.120 nonbonded pdb=" O LEU E 30 " pdb=" N THR E 34 " model vdw 2.180 3.120 nonbonded pdb=" O LEU C 366 " pdb=" OG1 THR C 370 " model vdw 2.181 3.040 ... (remaining 244556 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.800 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.580 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1255 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 0.070 30855 Z= 0.146 Angle : 0.524 7.226 41825 Z= 0.302 Chirality : 0.039 0.185 5190 Planarity : 0.004 0.097 5460 Dihedral : 12.804 89.678 11225 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % 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: 0.78 (0.13), residues: 4130 helix: 1.67 (0.12), residues: 1600 sheet: 0.15 (0.23), residues: 585 loop : -0.28 (0.15), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 423 TYR 0.019 0.002 TYR B 231 PHE 0.031 0.002 PHE B 203 TRP 0.003 0.001 TRP G 279 HIS 0.003 0.002 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00311 (30855) covalent geometry : angle 0.52374 (41825) hydrogen bonds : bond 0.09879 ( 1775) hydrogen bonds : angle 5.32728 ( 5046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 1.185 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: B 379 LYS cc_start: 0.3920 (ptpp) cc_final: 0.3711 (tttm) REVERT: C 106 GLN cc_start: 0.4594 (tt0) cc_final: 0.4010 (mt0) REVERT: C 154 GLU cc_start: 0.1382 (mt-10) cc_final: 0.1152 (mt-10) REVERT: C 296 TYR cc_start: 0.2120 (t80) cc_final: 0.1916 (t80) REVERT: F 57 ASN cc_start: 0.2021 (m110) cc_final: 0.1272 (t0) REVERT: G 113 THR cc_start: 0.2038 (p) cc_final: 0.1796 (t) REVERT: G 363 THR cc_start: 0.7393 (m) cc_final: 0.6976 (p) REVERT: G 422 TYR cc_start: 0.0939 (m-10) cc_final: 0.0318 (m-10) REVERT: H 48 GLN cc_start: 0.4079 (mp10) cc_final: 0.3556 (pp30) REVERT: J 316 ASN cc_start: 0.2310 (m110) cc_final: 0.1769 (t0) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.2117 time to fit residues: 151.7203 Evaluate side-chains 201 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 40 ASN A 191 ASN A 226 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 389 HIS C 40 ASN C 214 ASN C 217 ASN C 309 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 389 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 106 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 346 ASN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 106 GLN G 217 ASN G 331 ASN H 101 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN H 283 GLN H 338 ASN H 346 ASN H 362 ASN H 389 HIS ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 286 ASN J 389 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.255247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.223895 restraints weight = 49123.597| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 3.07 r_work: 0.4369 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.8373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.167 30855 Z= 0.414 Angle : 1.012 18.436 41825 Z= 0.550 Chirality : 0.055 0.440 5190 Planarity : 0.008 0.159 5460 Dihedral : 6.001 38.147 4330 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 2.19 % Allowed : 9.18 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % 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: -0.52 (0.13), residues: 4130 helix: 0.27 (0.12), residues: 1640 sheet: -0.61 (0.21), residues: 588 loop : -0.70 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG J 423 TYR 0.030 0.003 TYR G 209 PHE 0.047 0.004 PHE E 57 TRP 0.027 0.003 TRP E 279 HIS 0.005 0.002 HIS H 389 Details of bonding type rmsd covalent geometry : bond 0.00881 (30855) covalent geometry : angle 1.01239 (41825) hydrogen bonds : bond 0.06805 ( 1775) hydrogen bonds : angle 5.89919 ( 5046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 314 time to evaluate : 1.142 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: A 82 LEU cc_start: 0.8538 (tp) cc_final: 0.8326 (tp) REVERT: A 238 ARG cc_start: 0.7286 (mtp85) cc_final: 0.6854 (ttm-80) REVERT: B 97 VAL cc_start: 0.5892 (p) cc_final: 0.5535 (m) REVERT: B 379 LYS cc_start: 0.4579 (ptpp) cc_final: 0.4271 (tttm) REVERT: C 214 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6571 (t0) REVERT: C 296 TYR cc_start: 0.2830 (t80) cc_final: 0.2135 (t80) REVERT: E 138 ARG cc_start: 0.7784 (ptp-110) cc_final: 0.6135 (mtm180) REVERT: E 150 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5772 (t0) REVERT: E 436 TYR cc_start: 0.1427 (OUTLIER) cc_final: 0.0528 (t80) REVERT: F 170 LEU cc_start: 0.5768 (pp) cc_final: 0.5048 (tp) REVERT: F 173 LEU cc_start: 0.4545 (tp) cc_final: 0.4097 (tp) REVERT: F 445 ASN cc_start: 0.5113 (m-40) cc_final: 0.3942 (t0) REVERT: G 117 THR cc_start: 0.8295 (p) cc_final: 0.8085 (t) REVERT: G 138 ARG cc_start: 0.7956 (ptp-110) cc_final: 0.5110 (ptp-170) REVERT: H 48 GLN cc_start: 0.4668 (mp10) cc_final: 0.3658 (tm-30) REVERT: H 115 GLU cc_start: 0.3945 (tm-30) cc_final: 0.3639 (tp30) REVERT: I 64 LEU cc_start: 0.7264 (tp) cc_final: 0.6986 (tp) REVERT: I 436 TYR cc_start: 0.0707 (OUTLIER) cc_final: -0.0093 (t80) REVERT: J 316 ASN cc_start: 0.2168 (m110) cc_final: 0.1855 (t0) outliers start: 73 outliers final: 33 residues processed: 366 average time/residue: 0.1999 time to fit residues: 115.6208 Evaluate side-chains 229 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 336 SER Chi-restraints excluded: chain I residue 436 TYR Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 330 ASP Chi-restraints excluded: chain J residue 342 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 124 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 400 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 366 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 86 ASN D 147 GLN D 166 GLN ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN F 57 ASN ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.248071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.210327 restraints weight = 47433.727| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 3.33 r_work: 0.4186 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30855 Z= 0.162 Angle : 0.554 8.319 41825 Z= 0.302 Chirality : 0.041 0.355 5190 Planarity : 0.004 0.063 5460 Dihedral : 4.771 29.490 4330 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.43 % Allowed : 12.29 % Favored : 85.28 % 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: 0.21 (0.13), residues: 4130 helix: 0.97 (0.12), residues: 1655 sheet: 0.54 (0.24), residues: 475 loop : -0.61 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 119 TYR 0.028 0.002 TYR A 436 PHE 0.035 0.002 PHE B 433 TRP 0.010 0.001 TRP C 279 HIS 0.004 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00347 (30855) covalent geometry : angle 0.55405 (41825) hydrogen bonds : bond 0.04802 ( 1775) hydrogen bonds : angle 4.90490 ( 5046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 210 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 MET cc_start: -0.0592 (ppp) cc_final: -0.2761 (ttp) REVERT: B 379 LYS cc_start: 0.4706 (ptpp) cc_final: 0.4417 (tttm) REVERT: C 80 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7021 (tp30) REVERT: C 143 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: C 296 TYR cc_start: 0.3037 (t80) cc_final: 0.2294 (t80) REVERT: E 80 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7417 (mp0) REVERT: E 150 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.5969 (t0) REVERT: E 235 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: E 322 GLN cc_start: 0.4117 (OUTLIER) cc_final: 0.3598 (tm-30) REVERT: F 310 MET cc_start: 0.0759 (tpp) cc_final: 0.0039 (tpt) REVERT: F 332 TYR cc_start: 0.0962 (t80) cc_final: -0.0170 (t80) REVERT: H 48 GLN cc_start: 0.4697 (mp10) cc_final: 0.3538 (tm-30) REVERT: H 310 MET cc_start: 0.1035 (mmm) cc_final: 0.0683 (tpp) REVERT: I 436 TYR cc_start: 0.0648 (OUTLIER) cc_final: 0.0021 (t80) REVERT: J 316 ASN cc_start: 0.2384 (m110) cc_final: 0.1978 (t0) outliers start: 81 outliers final: 41 residues processed: 284 average time/residue: 0.1899 time to fit residues: 87.6483 Evaluate side-chains 206 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 61 ASN Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 436 TYR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 90 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 337 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 412 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 418 GLN H 434 ASN H 446 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.246246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.219105 restraints weight = 49449.854| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 2.61 r_work: 0.4373 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4331 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 1.0329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30855 Z= 0.175 Angle : 0.574 12.008 41825 Z= 0.310 Chirality : 0.042 0.228 5190 Planarity : 0.004 0.085 5460 Dihedral : 4.639 25.574 4330 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.97 % Allowed : 13.79 % Favored : 83.24 % 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: 0.31 (0.13), residues: 4130 helix: 1.16 (0.12), residues: 1655 sheet: 0.10 (0.21), residues: 605 loop : -0.56 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 93 TYR 0.023 0.002 TYR F 245 PHE 0.027 0.002 PHE E 57 TRP 0.003 0.001 TRP I 279 HIS 0.003 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00398 (30855) covalent geometry : angle 0.57427 (41825) hydrogen bonds : bond 0.04772 ( 1775) hydrogen bonds : angle 4.73767 ( 5046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 198 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 140 GLU cc_start: 0.7383 (pm20) cc_final: 0.7141 (pm20) REVERT: A 239 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8781 (mm110) REVERT: B 113 GLN cc_start: 0.5411 (tp40) cc_final: 0.4815 (pt0) REVERT: C 128 SER cc_start: 0.8258 (t) cc_final: 0.7984 (p) REVERT: C 143 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: C 296 TYR cc_start: 0.3053 (t80) cc_final: 0.2582 (t80) REVERT: D 310 MET cc_start: -0.1886 (tmm) cc_final: -0.2959 (pmm) REVERT: E 68 ASP cc_start: 0.8487 (m-30) cc_final: 0.8271 (m-30) REVERT: E 140 GLU cc_start: 0.7276 (pm20) cc_final: 0.6922 (pm20) REVERT: E 322 GLN cc_start: 0.5225 (OUTLIER) cc_final: 0.4731 (tm-30) REVERT: F 310 MET cc_start: 0.1152 (tpp) cc_final: 0.0558 (tpt) REVERT: F 332 TYR cc_start: 0.1180 (t80) cc_final: -0.0395 (t80) REVERT: G 116 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8440 (p) REVERT: G 384 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.7034 (p) REVERT: H 48 GLN cc_start: 0.4430 (mp10) cc_final: 0.3482 (tm-30) REVERT: I 264 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8997 (p) REVERT: I 436 TYR cc_start: 0.0869 (OUTLIER) cc_final: 0.0158 (t80) REVERT: J 245 TYR cc_start: 0.1130 (m-80) cc_final: 0.0717 (p90) outliers start: 99 outliers final: 47 residues processed: 276 average time/residue: 0.1958 time to fit residues: 87.4398 Evaluate side-chains 209 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 384 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 436 TYR Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 213 optimal weight: 3.9990 chunk 141 optimal weight: 40.0000 chunk 122 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 310 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN H 90 GLN H 104 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN I 217 ASN I 239 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN J 337 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.239173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.212020 restraints weight = 48510.663| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 2.41 r_work: 0.4255 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 1.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 30855 Z= 0.331 Angle : 0.724 14.099 41825 Z= 0.388 Chirality : 0.048 0.215 5190 Planarity : 0.005 0.091 5460 Dihedral : 5.274 30.674 4330 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.21 % Allowed : 16.13 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.24 (0.13), residues: 4130 helix: 0.68 (0.12), residues: 1620 sheet: -0.16 (0.22), residues: 565 loop : -0.83 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 238 TYR 0.031 0.002 TYR E 397 PHE 0.029 0.002 PHE B 433 TRP 0.019 0.003 TRP E 279 HIS 0.005 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00807 (30855) covalent geometry : angle 0.72442 (41825) hydrogen bonds : bond 0.05939 ( 1775) hydrogen bonds : angle 5.18394 ( 5046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 180 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.5736 (OUTLIER) cc_final: 0.4613 (p0) REVERT: A 239 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8855 (mm-40) REVERT: A 271 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (mmtp) REVERT: C 143 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: C 296 TYR cc_start: 0.4079 (t80) cc_final: 0.3403 (t80) REVERT: D 310 MET cc_start: -0.1931 (tmm) cc_final: -0.3304 (pmm) REVERT: E 82 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9085 (tp) REVERT: E 86 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9187 (m) REVERT: F 332 TYR cc_start: 0.1446 (t80) cc_final: 0.0453 (t80) REVERT: F 416 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5841 (mp) REVERT: G 274 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7656 (mm-30) REVERT: H 48 GLN cc_start: 0.4866 (mp10) cc_final: 0.3583 (tm-30) REVERT: I 140 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7583 (pm20) REVERT: I 384 THR cc_start: 0.8630 (m) cc_final: 0.8378 (p) outliers start: 107 outliers final: 65 residues processed: 274 average time/residue: 0.2016 time to fit residues: 89.2004 Evaluate side-chains 209 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 137 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 322 GLN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 213 THR Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 404 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 335 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 397 optimal weight: 0.6980 chunk 273 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 63 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN D 86 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 GLN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN J 337 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.241967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.209369 restraints weight = 47277.614| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 2.93 r_work: 0.4208 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 1.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30855 Z= 0.144 Angle : 0.521 9.211 41825 Z= 0.285 Chirality : 0.040 0.194 5190 Planarity : 0.004 0.076 5460 Dihedral : 4.581 23.244 4330 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 17.69 % Favored : 80.21 % 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: 0.27 (0.13), residues: 4130 helix: 1.21 (0.12), residues: 1640 sheet: 0.16 (0.23), residues: 565 loop : -0.67 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 93 TYR 0.019 0.001 TYR A 436 PHE 0.036 0.001 PHE B 433 TRP 0.004 0.001 TRP G 279 HIS 0.004 0.001 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00324 (30855) covalent geometry : angle 0.52064 (41825) hydrogen bonds : bond 0.04480 ( 1775) hydrogen bonds : angle 4.71433 ( 5046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 171 time to evaluate : 1.161 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: A 140 GLU cc_start: 0.7615 (pm20) cc_final: 0.6974 (pm20) REVERT: A 239 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8821 (mm-40) REVERT: A 271 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (mmtp) REVERT: A 290 PHE cc_start: 0.3890 (m-10) cc_final: 0.3672 (m-10) REVERT: C 143 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: C 296 TYR cc_start: 0.3934 (t80) cc_final: 0.3262 (t80) REVERT: C 326 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7292 (ptm160) REVERT: F 125 ARG cc_start: 0.7019 (ttp-170) cc_final: 0.6805 (mmp-170) REVERT: F 332 TYR cc_start: 0.1348 (t80) cc_final: 0.0423 (t80) REVERT: G 97 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9242 (mt) REVERT: G 274 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7709 (mm-30) REVERT: I 140 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7564 (pm20) outliers start: 70 outliers final: 50 residues processed: 230 average time/residue: 0.1962 time to fit residues: 73.5835 Evaluate side-chains 206 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 222 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 chunk 1 optimal weight: 8.9990 chunk 307 optimal weight: 0.8980 chunk 311 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 362 optimal weight: 0.4980 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN H 90 GLN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.239462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.207943 restraints weight = 46746.577| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.75 r_work: 0.4181 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 1.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 30855 Z= 0.220 Angle : 0.596 13.847 41825 Z= 0.320 Chirality : 0.043 0.213 5190 Planarity : 0.005 0.101 5460 Dihedral : 4.765 29.105 4330 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.46 % Allowed : 18.11 % Favored : 79.43 % 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: 0.21 (0.13), residues: 4130 helix: 1.20 (0.12), residues: 1630 sheet: 0.14 (0.21), residues: 665 loop : -0.79 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 93 TYR 0.019 0.002 TYR A 436 PHE 0.033 0.002 PHE B 433 TRP 0.006 0.002 TRP E 279 HIS 0.004 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00530 (30855) covalent geometry : angle 0.59551 (41825) hydrogen bonds : bond 0.04862 ( 1775) hydrogen bonds : angle 4.81388 ( 5046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 1.230 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: A 239 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8865 (mm-40) REVERT: A 271 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7917 (mmtp) REVERT: C 143 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: F 95 LEU cc_start: 0.6702 (pp) cc_final: 0.6495 (mp) REVERT: F 332 TYR cc_start: 0.1412 (t80) cc_final: 0.0336 (t80) REVERT: G 274 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7786 (mm-30) REVERT: I 140 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7594 (pm20) outliers start: 82 outliers final: 64 residues processed: 229 average time/residue: 0.1941 time to fit residues: 72.6407 Evaluate side-chains 209 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 340 THR Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 168 optimal weight: 2.9990 chunk 382 optimal weight: 0.5980 chunk 349 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 50.0000 chunk 317 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 239 GLN G 331 ASN H 90 GLN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 286 ASN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.241593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.206398 restraints weight = 45933.102| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.97 r_work: 0.4206 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 1.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30855 Z= 0.147 Angle : 0.517 9.614 41825 Z= 0.280 Chirality : 0.040 0.192 5190 Planarity : 0.003 0.064 5460 Dihedral : 4.437 23.820 4330 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.16 % Allowed : 18.68 % Favored : 79.16 % 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: 0.51 (0.13), residues: 4130 helix: 1.62 (0.12), residues: 1600 sheet: 0.26 (0.21), residues: 665 loop : -0.76 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 93 TYR 0.019 0.001 TYR A 436 PHE 0.031 0.001 PHE B 433 TRP 0.003 0.001 TRP G 279 HIS 0.003 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00338 (30855) covalent geometry : angle 0.51658 (41825) hydrogen bonds : bond 0.04256 ( 1775) hydrogen bonds : angle 4.59920 ( 5046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7652 (pm20) cc_final: 0.6968 (pm20) REVERT: A 239 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8861 (mm-40) REVERT: A 271 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7773 (mmtp) REVERT: A 276 ILE cc_start: 0.8015 (mm) cc_final: 0.7690 (mt) REVERT: C 143 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: D 410 GLN cc_start: 0.3237 (pp30) cc_final: 0.3003 (pp30) REVERT: F 177 GLN cc_start: 0.3425 (mp10) cc_final: 0.3207 (mp10) REVERT: F 332 TYR cc_start: 0.1372 (t80) cc_final: 0.0294 (t80) REVERT: G 274 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7876 (mm-30) REVERT: I 140 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7576 (pm20) outliers start: 72 outliers final: 60 residues processed: 225 average time/residue: 0.1891 time to fit residues: 70.3908 Evaluate side-chains 214 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 340 THR Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 140 optimal weight: 20.0000 chunk 120 optimal weight: 0.0870 chunk 237 optimal weight: 5.9990 chunk 392 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 226 optimal weight: 30.0000 chunk 299 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 151 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 239 GLN D 90 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** 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 = 0.4870 r_free = 0.4870 target = 0.242586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.215199 restraints weight = 48234.442| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 2.47 r_work: 0.4352 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.4319 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 1.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30855 Z= 0.123 Angle : 0.494 11.781 41825 Z= 0.268 Chirality : 0.039 0.196 5190 Planarity : 0.003 0.067 5460 Dihedral : 4.229 22.964 4330 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.13), residues: 4130 helix: 1.93 (0.12), residues: 1585 sheet: 0.37 (0.21), residues: 675 loop : -0.66 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 423 TYR 0.019 0.001 TYR A 436 PHE 0.029 0.001 PHE B 433 TRP 0.003 0.001 TRP C 279 HIS 0.003 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00274 (30855) covalent geometry : angle 0.49413 (41825) hydrogen bonds : bond 0.03980 ( 1775) hydrogen bonds : angle 4.45954 ( 5046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7440 (pm20) cc_final: 0.6915 (pm20) REVERT: A 147 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5241 (p0) REVERT: A 238 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7346 (mmm-85) REVERT: A 239 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8825 (mm-40) REVERT: A 271 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7673 (mmtp) REVERT: A 276 ILE cc_start: 0.7749 (mm) cc_final: 0.7484 (mt) REVERT: C 143 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: D 410 GLN cc_start: 0.2693 (pp30) cc_final: 0.2262 (pp30) REVERT: G 266 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8797 (p) REVERT: H 87 ASN cc_start: 0.6805 (m110) cc_final: 0.6574 (m-40) outliers start: 72 outliers final: 57 residues processed: 229 average time/residue: 0.2011 time to fit residues: 75.1284 Evaluate side-chains 217 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 340 THR Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 375 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 307 optimal weight: 0.0000 chunk 358 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 268 optimal weight: 0.2980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 83 ASN ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.243907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.217673 restraints weight = 48431.868| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 2.40 r_work: 0.4365 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4314 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 1.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30855 Z= 0.116 Angle : 0.498 15.047 41825 Z= 0.266 Chirality : 0.039 0.230 5190 Planarity : 0.003 0.056 5460 Dihedral : 4.141 23.224 4330 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 19.19 % Favored : 78.95 % 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: 0.95 (0.13), residues: 4130 helix: 2.14 (0.12), residues: 1560 sheet: 0.51 (0.21), residues: 685 loop : -0.62 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 423 TYR 0.019 0.001 TYR A 436 PHE 0.030 0.001 PHE B 433 TRP 0.004 0.001 TRP G 279 HIS 0.003 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00253 (30855) covalent geometry : angle 0.49779 (41825) hydrogen bonds : bond 0.03877 ( 1775) hydrogen bonds : angle 4.39016 ( 5046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 1.378 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: A 140 GLU cc_start: 0.7471 (pm20) cc_final: 0.6933 (pm20) REVERT: A 147 ASP cc_start: 0.5733 (OUTLIER) cc_final: 0.5254 (p0) REVERT: A 238 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7297 (mmm-85) REVERT: A 239 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8822 (mm-40) REVERT: A 271 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7615 (mmtp) REVERT: A 276 ILE cc_start: 0.7783 (mm) cc_final: 0.7514 (mt) REVERT: A 358 ASP cc_start: 0.6675 (p0) cc_final: 0.6408 (p0) REVERT: C 143 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: D 410 GLN cc_start: 0.2797 (pp30) cc_final: 0.2412 (pp30) REVERT: G 266 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8813 (p) REVERT: H 332 TYR cc_start: 0.0854 (OUTLIER) cc_final: -0.0624 (t80) REVERT: I 86 THR cc_start: 0.9358 (t) cc_final: 0.8964 (m) outliers start: 62 outliers final: 53 residues processed: 212 average time/residue: 0.1889 time to fit residues: 66.8827 Evaluate side-chains 212 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 389 HIS Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 340 THR Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 216 optimal weight: 8.9990 chunk 327 optimal weight: 30.0000 chunk 194 optimal weight: 5.9990 chunk 202 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 287 optimal weight: 3.9990 chunk 351 optimal weight: 0.6980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** J 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.242998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.218674 restraints weight = 48508.456| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 2.20 r_work: 0.4370 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4307 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 1.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30855 Z= 0.128 Angle : 0.501 11.596 41825 Z= 0.268 Chirality : 0.039 0.198 5190 Planarity : 0.004 0.072 5460 Dihedral : 4.170 26.642 4330 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.01 % Allowed : 19.28 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.13), residues: 4130 helix: 2.18 (0.12), residues: 1570 sheet: 0.44 (0.22), residues: 635 loop : -0.59 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 125 TYR 0.019 0.001 TYR A 436 PHE 0.030 0.001 PHE B 433 TRP 0.004 0.001 TRP G 279 HIS 0.003 0.001 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00290 (30855) covalent geometry : angle 0.50081 (41825) hydrogen bonds : bond 0.03896 ( 1775) hydrogen bonds : angle 4.36698 ( 5046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8233.17 seconds wall clock time: 142 minutes 33.37 seconds (8553.37 seconds total)