Starting phenix.real_space_refine on Sat Jul 4 06:04:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e6k_27921/07_2026/8e6k_27921.cif" } resolution = 3.1 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= 0.018 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 120 5.16 5 C 11908 2.51 5 N 3200 2.21 5 O 3704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18932 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, I, J, K, E, F, G Time building chain proxies: 3.58, per 1000 atoms: 0.19 Number of scatterers: 18932 At special positions: 0 Unit cell: (166.025, 166.025, 82.65, 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 120 16.00 O 3704 8.00 N 3200 7.00 C 11908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.05 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.05 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.05 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.05 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG B 501 " - " ASN B 146 " " NAG C 501 " - " ASN C 146 " " NAG D 501 " - " ASN D 146 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 681.0 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 5.2% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER A 145 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER B 145 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER C 145 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 146 " --> pdb=" O LYS C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER D 145 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA A 203 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 205 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR A 252 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU A 267 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 254 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS A 256 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER A 372 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 400 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET A 376 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP A 396 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 394 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 205 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR B 252 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 267 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 254 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 256 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER B 372 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 400 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET B 376 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 396 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP B 378 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG B 394 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR E 52 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR E 34 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA C 203 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 205 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR C 252 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 267 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 254 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS C 256 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER C 372 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE C 400 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET C 376 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP C 396 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP C 378 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG C 394 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'F' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP F 35A" --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR F 52 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR F 34 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA D 203 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR D 214 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 205 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR D 252 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU D 267 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 254 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS D 256 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER D 372 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE D 400 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET D 376 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP D 396 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP D 378 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG D 394 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP G 35A" --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR G 52 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR G 34 " --> pdb=" O TYR G 52 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1692 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: 3.76 Time building geometry restraints manager: 2.11 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: 6036 1.34 - 1.47: 5156 1.47 - 1.59: 8084 1.59 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 19432 Sorted by residual: bond pdb=" N VAL L 15 " pdb=" CA VAL L 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL I 15 " pdb=" CA VAL I 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL J 15 " pdb=" CA VAL J 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N ARG J 18 " pdb=" CA ARG J 18 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.34e+00 ... (remaining 19427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 22076 1.28 - 2.57: 3172 2.57 - 3.85: 756 3.85 - 5.14: 340 5.14 - 6.42: 96 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N ASN C 299 " pdb=" CA ASN C 299 " pdb=" C ASN C 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN B 299 " pdb=" CA ASN B 299 " pdb=" C ASN B 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN A 299 " pdb=" CA ASN A 299 " pdb=" C ASN A 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN D 299 " pdb=" CA ASN D 299 " pdb=" C ASN D 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" C CYS A 318 " pdb=" N SER A 319 " pdb=" CA SER A 319 " ideal model delta sigma weight residual 121.31 125.98 -4.67 1.49e+00 4.50e-01 9.81e+00 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 10372 15.95 - 31.89: 716 31.89 - 47.84: 232 47.84 - 63.79: 68 63.79 - 79.73: 20 Dihedral angle restraints: 11408 sinusoidal: 4436 harmonic: 6972 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 11405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1696 0.048 - 0.096: 736 0.096 - 0.144: 360 0.144 - 0.192: 52 0.192 - 0.240: 12 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2853 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG D 501 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.179 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " -0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG A 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG B 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.018 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1008 2.71 - 3.26: 17576 3.26 - 3.81: 31552 3.81 - 4.35: 41908 4.35 - 4.90: 72448 Nonbonded interactions: 164492 Sorted by model distance: nonbonded pdb=" OD2 ASP D 293 " pdb=" OH TYR D 316 " model vdw 2.167 3.040 nonbonded pdb=" OD2 ASP B 293 " pdb=" OH TYR B 316 " model vdw 2.167 3.040 nonbonded pdb=" OD2 ASP A 293 " pdb=" OH TYR A 316 " model vdw 2.167 3.040 nonbonded pdb=" OD2 ASP C 293 " pdb=" OH TYR C 316 " model vdw 2.167 3.040 nonbonded pdb=" O GLN L 6 " pdb=" NE2 GLN L 100 " model vdw 2.259 3.120 ... (remaining 164487 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'L' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.006 0.051 19476 Z= 0.284 Angle : 1.118 6.424 26532 Z= 0.624 Chirality : 0.064 0.240 2856 Planarity : 0.007 0.111 3400 Dihedral : 13.365 79.733 6864 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.19 % Allowed : 13.26 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.50 (0.16), residues: 2432 helix: 0.30 (0.83), residues: 24 sheet: 0.80 (0.16), residues: 944 loop : 0.08 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 327 TYR 0.047 0.004 TYR K 92 PHE 0.046 0.005 PHE A 410 TRP 0.037 0.003 TRP B 456 HIS 0.006 0.002 HIS B 412A Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (19432) covalent geometry : angle 1.11164 / 0.62 (26440) SS BOND : bond 0.01004 / 0.65 ( 40) SS BOND : angle 2.33779 / 1.55 ( 80) hydrogen bonds : bond 0.13603 / 9.53 ( 672) hydrogen bonds : angle 8.72701 / 6.09 ( 1692) link_NAG-ASN : bond 0.00025 / 0.01 ( 4) link_NAG-ASN : angle 1.84185 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 344 time to evaluate : 0.731 Fit side-chains REVERT: A 150 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7033 (tppt) REVERT: B 150 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7035 (tppt) REVERT: C 150 LYS cc_start: 0.7324 (ttpt) cc_final: 0.7033 (tppt) REVERT: D 150 LYS cc_start: 0.7328 (ttpt) cc_final: 0.7035 (tppt) outliers start: 4 outliers final: 0 residues processed: 348 average time/residue: 0.1227 time to fit residues: 66.8561 Evaluate side-chains 240 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 235 optimal weight: 7.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN B 136 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN C 136 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN D 136 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144327 restraints weight = 22624.183| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.45 r_work: 0.3666 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19476 Z= 0.137 Angle : 0.651 6.422 26532 Z= 0.352 Chirality : 0.048 0.142 2856 Planarity : 0.004 0.039 3400 Dihedral : 5.215 24.957 2644 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.65 % Allowed : 12.50 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.77 (0.17), residues: 2432 helix: -0.68 (0.79), residues: 24 sheet: 0.97 (0.16), residues: 952 loop : 0.31 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 419 TYR 0.017 0.002 TYR J 92 PHE 0.020 0.002 PHE B 410 TRP 0.014 0.002 TRP B 456 HIS 0.008 0.002 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (19432) covalent geometry : angle 0.64845 / 0.35 (26440) SS BOND : bond 0.00427 / 0.30 ( 40) SS BOND : angle 1.16216 / 0.74 ( 80) hydrogen bonds : bond 0.04341 / 2.97 ( 672) hydrogen bonds : angle 7.23954 / 5.06 ( 1692) link_NAG-ASN : bond 0.00170 / 0.08 ( 4) link_NAG-ASN : angle 0.94489 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 304 average time/residue: 0.1114 time to fit residues: 55.5639 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 185 optimal weight: 0.9980 chunk 239 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS H 1 GLN B 126 HIS ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS E 1 GLN C 126 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS F 1 GLN D 126 HIS ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS G 1 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141243 restraints weight = 22234.401| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.51 r_work: 0.3636 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19476 Z= 0.123 Angle : 0.591 6.228 26532 Z= 0.316 Chirality : 0.047 0.146 2856 Planarity : 0.004 0.044 3400 Dihedral : 5.019 29.983 2644 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.46 % Allowed : 13.45 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.80 (0.17), residues: 2432 helix: -0.95 (0.80), residues: 24 sheet: 0.99 (0.16), residues: 960 loop : 0.32 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.014 0.001 TYR D 252 PHE 0.018 0.002 PHE D 410 TRP 0.012 0.001 TRP B 456 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (19432) covalent geometry : angle 0.58969 / 0.32 (26440) SS BOND : bond 0.00453 / 0.29 ( 40) SS BOND : angle 0.80809 / 0.53 ( 80) hydrogen bonds : bond 0.03777 / 2.59 ( 672) hydrogen bonds : angle 6.73393 / 4.73 ( 1692) link_NAG-ASN : bond 0.00034 / 0.02 ( 4) link_NAG-ASN : angle 0.97964 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 32 residues processed: 276 average time/residue: 0.1198 time to fit residues: 53.4379 Evaluate side-chains 248 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137140 restraints weight = 22513.892| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.45 r_work: 0.3597 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19476 Z= 0.155 Angle : 0.626 8.553 26532 Z= 0.328 Chirality : 0.048 0.148 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.076 31.873 2644 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 14.02 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.72 (0.17), residues: 2432 helix: -1.15 (0.77), residues: 28 sheet: 1.14 (0.17), residues: 936 loop : 0.14 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 419 TYR 0.014 0.002 TYR L 92 PHE 0.018 0.002 PHE A 410 TRP 0.012 0.002 TRP B 456 HIS 0.004 0.002 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (19432) covalent geometry : angle 0.61653 / 0.32 (26440) SS BOND : bond 0.00436 / 0.29 ( 40) SS BOND : angle 2.02922 / 1.18 ( 80) hydrogen bonds : bond 0.03550 / 2.43 ( 672) hydrogen bonds : angle 6.60716 / 4.66 ( 1692) link_NAG-ASN : bond 0.00066 / 0.03 ( 4) link_NAG-ASN : angle 0.93084 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 430 GLN cc_start: 0.7374 (tp40) cc_final: 0.7056 (mm-40) REVERT: B 99 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 430 GLN cc_start: 0.7373 (tp40) cc_final: 0.7053 (mm-40) REVERT: C 99 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8089 (tt) REVERT: C 430 GLN cc_start: 0.7379 (tp40) cc_final: 0.7059 (mm-40) REVERT: D 99 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8090 (tt) REVERT: D 430 GLN cc_start: 0.7366 (tp40) cc_final: 0.7045 (mm-40) outliers start: 64 outliers final: 48 residues processed: 280 average time/residue: 0.1155 time to fit residues: 53.3951 Evaluate side-chains 256 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 252 TYR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 202 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134307 restraints weight = 22522.407| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.43 r_work: 0.3562 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19476 Z= 0.161 Angle : 0.604 6.089 26532 Z= 0.320 Chirality : 0.048 0.156 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.099 28.195 2644 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.41 % Allowed : 14.39 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.67 (0.17), residues: 2432 helix: -1.15 (0.78), residues: 28 sheet: 1.08 (0.17), residues: 924 loop : 0.13 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.012 0.002 TYR L 92 PHE 0.016 0.002 PHE D 410 TRP 0.013 0.002 TRP A 456 HIS 0.005 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (19432) covalent geometry : angle 0.59644 / 0.32 (26440) SS BOND : bond 0.00300 / 0.19 ( 40) SS BOND : angle 1.81915 / 1.09 ( 80) hydrogen bonds : bond 0.03500 / 2.40 ( 672) hydrogen bonds : angle 6.53419 / 4.61 ( 1692) link_NAG-ASN : bond 0.00010 / 0.00 ( 4) link_NAG-ASN : angle 1.06872 / 0.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8133 (tt) REVERT: H 7 SER cc_start: 0.8119 (t) cc_final: 0.7912 (m) REVERT: B 99 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8133 (tt) REVERT: E 7 SER cc_start: 0.8114 (t) cc_final: 0.7911 (m) REVERT: C 99 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8154 (tt) REVERT: F 7 SER cc_start: 0.8105 (t) cc_final: 0.7900 (m) REVERT: D 99 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 72 outliers final: 48 residues processed: 288 average time/residue: 0.1106 time to fit residues: 52.5102 Evaluate side-chains 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 219 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 186 optimal weight: 0.0470 chunk 200 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135801 restraints weight = 22322.988| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.45 r_work: 0.3583 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19476 Z= 0.128 Angle : 0.572 5.638 26532 Z= 0.302 Chirality : 0.046 0.158 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.029 32.030 2644 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.38 % Rotamer: Outliers : 2.84 % Allowed : 15.01 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.67 (0.17), residues: 2432 helix: -0.98 (0.80), residues: 28 sheet: 1.01 (0.17), residues: 944 loop : 0.16 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 327 TYR 0.011 0.001 TYR I 96 PHE 0.013 0.002 PHE F 78 TRP 0.014 0.001 TRP A 178 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19432) covalent geometry : angle 0.56418 / 0.30 (26440) SS BOND : bond 0.00466 / 0.29 ( 40) SS BOND : angle 1.74116 / 1.04 ( 80) hydrogen bonds : bond 0.03291 / 2.26 ( 672) hydrogen bonds : angle 6.40520 / 4.51 ( 1692) link_NAG-ASN : bond 0.00038 / 0.02 ( 4) link_NAG-ASN : angle 1.07846 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8124 (tt) REVERT: L 42 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7689 (mmmt) REVERT: B 99 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8122 (tt) REVERT: I 42 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7691 (mmmt) REVERT: C 99 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8141 (tt) REVERT: J 42 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7689 (mmmt) REVERT: D 99 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8138 (tt) REVERT: K 42 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7685 (mmmt) outliers start: 60 outliers final: 44 residues processed: 271 average time/residue: 0.1162 time to fit residues: 51.2935 Evaluate side-chains 260 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 109 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139867 restraints weight = 22753.144| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.39 r_work: 0.3619 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19476 Z= 0.106 Angle : 0.545 5.878 26532 Z= 0.287 Chirality : 0.045 0.159 2856 Planarity : 0.004 0.029 3400 Dihedral : 4.862 29.795 2644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 15.34 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.82 (0.18), residues: 2432 helix: -1.05 (0.77), residues: 28 sheet: 1.12 (0.17), residues: 944 loop : 0.26 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 419 TYR 0.011 0.001 TYR A 275 PHE 0.013 0.002 PHE G 78 TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (19432) covalent geometry : angle 0.53972 / 0.29 (26440) SS BOND : bond 0.00291 / 0.20 ( 40) SS BOND : angle 1.43306 / 0.86 ( 80) hydrogen bonds : bond 0.03102 / 2.13 ( 672) hydrogen bonds : angle 6.19870 / 4.36 ( 1692) link_NAG-ASN : bond 0.00066 / 0.03 ( 4) link_NAG-ASN : angle 1.03249 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 42 LYS cc_start: 0.7855 (mmmm) cc_final: 0.7629 (mmmt) REVERT: I 42 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7632 (mmmt) REVERT: J 42 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7640 (mmmt) REVERT: K 42 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7633 (mmmt) outliers start: 64 outliers final: 48 residues processed: 264 average time/residue: 0.1163 time to fit residues: 50.4463 Evaluate side-chains 252 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137010 restraints weight = 22801.410| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.41 r_work: 0.3582 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19476 Z= 0.133 Angle : 0.558 5.682 26532 Z= 0.295 Chirality : 0.046 0.155 2856 Planarity : 0.004 0.030 3400 Dihedral : 4.902 29.013 2644 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.38 % Rotamer: Outliers : 2.65 % Allowed : 15.53 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.77 (0.18), residues: 2432 helix: -0.76 (0.79), residues: 28 sheet: 0.99 (0.17), residues: 964 loop : 0.28 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.011 0.001 TYR I 96 PHE 0.014 0.002 PHE H 78 TRP 0.015 0.001 TRP C 97 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (19432) covalent geometry : angle 0.55185 / 0.29 (26440) SS BOND : bond 0.00311 / 0.20 ( 40) SS BOND : angle 1.51959 / 0.92 ( 80) hydrogen bonds : bond 0.03158 / 2.18 ( 672) hydrogen bonds : angle 6.24993 / 4.40 ( 1692) link_NAG-ASN : bond 0.00095 / 0.04 ( 4) link_NAG-ASN : angle 0.96149 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8169 (tt) REVERT: L 42 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7657 (mmmt) REVERT: B 99 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8169 (tt) REVERT: I 42 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7657 (mmmt) REVERT: C 99 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8181 (tt) REVERT: J 42 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7656 (mmmt) REVERT: D 99 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8169 (tt) REVERT: K 42 LYS cc_start: 0.7862 (mmmm) cc_final: 0.7648 (mmmt) outliers start: 56 outliers final: 44 residues processed: 256 average time/residue: 0.1108 time to fit residues: 47.2966 Evaluate side-chains 256 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 139 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 227 optimal weight: 0.0070 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137106 restraints weight = 22736.959| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.40 r_work: 0.3592 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19476 Z= 0.122 Angle : 0.551 5.905 26532 Z= 0.290 Chirality : 0.046 0.155 2856 Planarity : 0.004 0.029 3400 Dihedral : 4.878 28.331 2644 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 3.03 % Allowed : 15.34 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.79 (0.18), residues: 2432 helix: -0.70 (0.79), residues: 28 sheet: 1.02 (0.17), residues: 960 loop : 0.29 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.017 0.001 TYR D 275 PHE 0.013 0.002 PHE F 78 TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (19432) covalent geometry : angle 0.54578 / 0.29 (26440) SS BOND : bond 0.00304 / 0.20 ( 40) SS BOND : angle 1.43997 / 0.87 ( 80) hydrogen bonds : bond 0.03126 / 2.15 ( 672) hydrogen bonds : angle 6.21882 / 4.37 ( 1692) link_NAG-ASN : bond 0.00090 / 0.04 ( 4) link_NAG-ASN : angle 0.99411 / 0.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8156 (tt) REVERT: L 42 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7675 (mmmt) REVERT: B 99 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8154 (tt) REVERT: I 42 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7680 (mmmt) REVERT: C 99 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8167 (tt) REVERT: J 42 LYS cc_start: 0.7888 (mmmm) cc_final: 0.7680 (mmmt) REVERT: D 99 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8159 (tt) REVERT: K 42 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7678 (mmmt) outliers start: 64 outliers final: 48 residues processed: 260 average time/residue: 0.1059 time to fit residues: 45.6419 Evaluate side-chains 252 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 168 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136948 restraints weight = 22775.017| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.43 r_work: 0.3587 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19476 Z= 0.128 Angle : 0.577 9.503 26532 Z= 0.297 Chirality : 0.046 0.154 2856 Planarity : 0.004 0.050 3400 Dihedral : 4.976 35.999 2644 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 16.29 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.75 (0.18), residues: 2432 helix: -0.61 (0.79), residues: 28 sheet: 0.98 (0.17), residues: 960 loop : 0.28 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.016 0.001 TYR D 275 PHE 0.013 0.002 PHE F 78 TRP 0.012 0.001 TRP C 97 HIS 0.004 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19432) covalent geometry : angle 0.56934 / 0.29 (26440) SS BOND : bond 0.00533 / 0.33 ( 40) SS BOND : angle 1.78660 / 1.06 ( 80) hydrogen bonds : bond 0.03105 / 2.14 ( 672) hydrogen bonds : angle 6.21084 / 4.37 ( 1692) link_NAG-ASN : bond 0.00093 / 0.04 ( 4) link_NAG-ASN : angle 1.01080 / 0.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 42 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7685 (mmmt) REVERT: I 42 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7683 (mmmt) REVERT: J 42 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7681 (mmmt) REVERT: K 42 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7677 (mmmt) outliers start: 52 outliers final: 52 residues processed: 248 average time/residue: 0.1136 time to fit residues: 46.1423 Evaluate side-chains 252 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 54 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 144 optimal weight: 0.0020 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137782 restraints weight = 22871.971| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.40 r_work: 0.3598 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19476 Z= 0.116 Angle : 0.554 6.260 26532 Z= 0.290 Chirality : 0.046 0.154 2856 Planarity : 0.004 0.044 3400 Dihedral : 4.915 35.279 2644 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.38 % Rotamer: Outliers : 2.84 % Allowed : 16.10 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.79 (0.17), residues: 2432 helix: -0.52 (0.79), residues: 28 sheet: 1.09 (0.17), residues: 940 loop : 0.25 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.015 0.001 TYR D 275 PHE 0.012 0.002 PHE G 78 TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19432) covalent geometry : angle 0.54700 / 0.29 (26440) SS BOND : bond 0.00455 / 0.29 ( 40) SS BOND : angle 1.67809 / 1.00 ( 80) hydrogen bonds : bond 0.03082 / 2.12 ( 672) hydrogen bonds : angle 6.16965 / 4.34 ( 1692) link_NAG-ASN : bond 0.00099 / 0.05 ( 4) link_NAG-ASN : angle 1.00020 / 0.64 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4553.73 seconds wall clock time: 78 minutes 59.49 seconds (4739.49 seconds total)