Starting phenix.real_space_refine on Sun Aug 24 09:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_27921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_27921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_27921.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_27921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6k_27921/08_2025/8e6k_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, I, J, K, E, F, G Time building chain proxies: 2.70, per 1000 atoms: 0.14 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: 1.56 Conformation dependent library (CDL) restraints added in 839.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.57 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: 3.23 Time building geometry restraints manager: 2.08 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: 10448 15.95 - 31.89: 716 31.89 - 47.84: 240 47.84 - 63.79: 68 63.79 - 79.73: 20 Dihedral angle restraints: 11492 sinusoidal: 4520 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 11489 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: 0.06 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 13.346 79.733 6948 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 aren 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 covalent geometry : bond 0.00642 (19432) covalent geometry : angle 1.11164 (26440) SS BOND : bond 0.01004 ( 40) SS BOND : angle 2.33779 ( 80) hydrogen bonds : bond 0.13603 ( 672) hydrogen bonds : angle 8.72701 ( 1692) link_NAG-ASN : bond 0.00025 ( 4) link_NAG-ASN : angle 1.84185 ( 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 : 0.711 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: 0.1202 time to fit residues: 65.3001 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 : 0.730 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.161755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144495 restraints weight = 22614.280| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.43 r_work: 0.3669 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1303 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= 0.135 Angle : 0.646 6.261 26532 Z= 0.350 Chirality : 0.048 0.142 2856 Planarity : 0.004 0.038 3400 Dihedral : 5.263 25.201 2728 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.65 % Allowed : 12.31 % Favored : 85.04 % 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 aren not related in a simple way. whole: 0.77 (0.17), residues: 2432 helix: -0.71 (0.79), residues: 24 sheet: 0.96 (0.16), residues: 952 loop : 0.32 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 419 TYR 0.018 0.002 TYR J 92 PHE 0.019 0.002 PHE B 410 TRP 0.014 0.002 TRP B 456 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00302 (19432) covalent geometry : angle 0.64479 (26440) SS BOND : bond 0.00396 ( 40) SS BOND : angle 0.95802 ( 80) hydrogen bonds : bond 0.04308 ( 672) hydrogen bonds : angle 7.21949 ( 1692) link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 1.08065 ( 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 : 0.717 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: 0.1107 time to fit residues: 54.9867 Evaluate side-chains 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3824 r_free = 0.3824 target = 0.151028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133321 restraints weight = 22469.465| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.44 r_work: 0.3554 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19476 Z= 0.186 Angle : 0.651 6.573 26532 Z= 0.348 Chirality : 0.050 0.154 2856 Planarity : 0.005 0.048 3400 Dihedral : 5.270 30.313 2728 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.60 % Allowed : 13.07 % Favored : 83.33 % 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 aren not related in a simple way. whole: 0.69 (0.17), residues: 2432 helix: -1.12 (0.73), residues: 28 sheet: 1.17 (0.17), residues: 904 loop : 0.09 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.018 0.002 TYR J 92 PHE 0.022 0.003 PHE D 115 TRP 0.017 0.002 TRP B 456 HIS 0.006 0.002 HIS B 412A Details of bonding type rmsd covalent geometry : bond 0.00436 (19432) covalent geometry : angle 0.65069 (26440) SS BOND : bond 0.00375 ( 40) SS BOND : angle 0.79861 ( 80) hydrogen bonds : bond 0.04004 ( 672) hydrogen bonds : angle 6.89202 ( 1692) link_NAG-ASN : bond 0.00019 ( 4) link_NAG-ASN : angle 0.94842 ( 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 304 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 56 residues processed: 288 average time/residue: 0.1102 time to fit residues: 51.4999 Evaluate side-chains 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 TYR 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 L residue 74 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 116 VAL Chi-restraints excluded: chain B residue 157 THR 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 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 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 116 VAL Chi-restraints excluded: chain C residue 157 THR 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 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 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 116 VAL Chi-restraints excluded: chain D residue 157 THR 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 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3870 r_free = 0.3870 target = 0.154976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137568 restraints weight = 22404.931| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.42 r_work: 0.3608 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2233 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= 0.113 Angle : 0.572 5.993 26532 Z= 0.303 Chirality : 0.046 0.157 2856 Planarity : 0.004 0.030 3400 Dihedral : 5.051 31.948 2728 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.46 % Allowed : 14.96 % Favored : 82.58 % 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 aren not related in a simple way. whole: 0.75 (0.17), residues: 2432 helix: -1.22 (0.73), residues: 28 sheet: 1.21 (0.17), residues: 900 loop : 0.14 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.010 0.001 TYR I 92 PHE 0.014 0.002 PHE D 410 TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00252 (19432) covalent geometry : angle 0.56895 (26440) SS BOND : bond 0.00681 ( 40) SS BOND : angle 1.14277 ( 80) hydrogen bonds : bond 0.03427 ( 672) hydrogen bonds : angle 6.59088 ( 1692) link_NAG-ASN : bond 0.00044 ( 4) link_NAG-ASN : angle 1.08799 ( 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 284 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.716 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: 0.1167 time to fit residues: 52.9776 Evaluate side-chains 236 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER 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 B residue 90 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 C residue 90 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 D residue 90 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 9.9990 chunk 174 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 202 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3857 r_free = 0.3857 target = 0.153861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136339 restraints weight = 22497.517| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.44 r_work: 0.3598 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2404 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= 0.132 Angle : 0.598 10.429 26532 Z= 0.314 Chirality : 0.047 0.158 2856 Planarity : 0.004 0.029 3400 Dihedral : 5.036 28.835 2728 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.84 % Allowed : 14.77 % Favored : 82.39 % 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 aren not related in a simple way. whole: 0.75 (0.17), residues: 2432 helix: -1.09 (0.79), residues: 28 sheet: 1.18 (0.17), residues: 924 loop : 0.15 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.011 0.001 TYR I 92 PHE 0.014 0.002 PHE C 410 TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00310 (19432) covalent geometry : angle 0.58408 (26440) SS BOND : bond 0.00299 ( 40) SS BOND : angle 2.36779 ( 80) hydrogen bonds : bond 0.03353 ( 672) hydrogen bonds : angle 6.48365 ( 1692) link_NAG-ASN : bond 0.00008 ( 4) link_NAG-ASN : angle 1.10827 ( 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 280 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 42 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7615 (mmmt) REVERT: I 42 LYS cc_start: 0.7830 (mmmm) cc_final: 0.7610 (mmmt) REVERT: J 42 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7607 (mmmt) REVERT: K 42 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7605 (mmmt) outliers start: 60 outliers final: 44 residues processed: 268 average time/residue: 0.1141 time to fit residues: 49.9273 Evaluate side-chains 244 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 116 VAL 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 H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 VAL 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 E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 116 VAL 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 F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 116 VAL 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 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: 10.0000 chunk 239 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 172 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3769 r_free = 0.3769 target = 0.146718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128646 restraints weight = 22845.891| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.46 r_work: 0.3482 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19476 Z= 0.237 Angle : 0.677 8.681 26532 Z= 0.361 Chirality : 0.051 0.172 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.408 33.785 2728 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 3.22 % Allowed : 15.34 % Favored : 81.44 % 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 aren not related in a simple way. whole: 0.48 (0.17), residues: 2432 helix: -0.92 (0.87), residues: 28 sheet: 0.82 (0.17), residues: 944 loop : 0.08 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 394 TYR 0.015 0.002 TYR L 92 PHE 0.018 0.003 PHE C 410 TRP 0.019 0.002 TRP D 97 HIS 0.007 0.003 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00569 (19432) covalent geometry : angle 0.66447 (26440) SS BOND : bond 0.00457 ( 40) SS BOND : angle 2.42638 ( 80) hydrogen bonds : bond 0.03800 ( 672) hydrogen bonds : angle 6.81063 ( 1692) link_NAG-ASN : bond 0.00008 ( 4) link_NAG-ASN : angle 1.07556 ( 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 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 204 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.7790 (p90) REVERT: B 155 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 155 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7792 (p90) REVERT: D 155 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7785 (p90) outliers start: 68 outliers final: 52 residues processed: 264 average time/residue: 0.1194 time to fit residues: 51.9692 Evaluate side-chains 248 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS 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 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 90 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS 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 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 90 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS 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 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 90 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3807 r_free = 0.3807 target = 0.149554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132086 restraints weight = 22672.343| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.42 r_work: 0.3540 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19476 Z= 0.142 Angle : 0.593 5.982 26532 Z= 0.315 Chirality : 0.047 0.150 2856 Planarity : 0.004 0.035 3400 Dihedral : 5.151 31.064 2728 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 2.65 % Allowed : 16.10 % 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 aren not related in a simple way. whole: 0.53 (0.17), residues: 2432 helix: -0.90 (0.85), residues: 28 sheet: 0.83 (0.17), residues: 940 loop : 0.14 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 292 TYR 0.012 0.001 TYR I 96 PHE 0.013 0.002 PHE A 422 TRP 0.016 0.002 TRP C 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00339 (19432) covalent geometry : angle 0.58487 (26440) SS BOND : bond 0.00356 ( 40) SS BOND : angle 1.78518 ( 80) hydrogen bonds : bond 0.03370 ( 672) hydrogen bonds : angle 6.54282 ( 1692) link_NAG-ASN : bond 0.00058 ( 4) link_NAG-ASN : angle 1.15542 ( 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 276 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 48 residues processed: 264 average time/residue: 0.1203 time to fit residues: 51.9711 Evaluate side-chains 244 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 332 THR 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 7 SER 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 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 CYS 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 437 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 7 SER 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 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 230 CYS 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 437 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 7 SER 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 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 230 CYS 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 437 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 7 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 82 optimal weight: 0.0040 chunk 214 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 132 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 overall best weight: 0.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3808 r_free = 0.3808 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132443 restraints weight = 22628.663| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.41 r_work: 0.3539 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19476 Z= 0.148 Angle : 0.587 5.760 26532 Z= 0.310 Chirality : 0.047 0.150 2856 Planarity : 0.004 0.030 3400 Dihedral : 5.059 30.039 2728 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer: Outliers : 3.22 % Allowed : 16.86 % Favored : 79.92 % 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 aren not related in a simple way. whole: 0.56 (0.18), residues: 2432 helix: -1.01 (0.79), residues: 28 sheet: 0.90 (0.17), residues: 944 loop : 0.12 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 327 TYR 0.012 0.001 TYR I 96 PHE 0.014 0.002 PHE L 71 TRP 0.014 0.001 TRP C 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00358 (19432) covalent geometry : angle 0.57983 (26440) SS BOND : bond 0.00362 ( 40) SS BOND : angle 1.73390 ( 80) hydrogen bonds : bond 0.03345 ( 672) hydrogen bonds : angle 6.44155 ( 1692) link_NAG-ASN : bond 0.00019 ( 4) link_NAG-ASN : angle 1.13728 ( 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 292 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7556 (p90) REVERT: B 155 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7559 (p90) REVERT: C 155 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7565 (p90) REVERT: D 155 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7553 (p90) outliers start: 68 outliers final: 48 residues processed: 280 average time/residue: 0.1231 time to fit residues: 55.6777 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 : 0.721 ------------------------------------------------------------------------------- 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 155 TYR 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 7 SER 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 155 TYR 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 7 SER 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 155 TYR 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 7 SER 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 155 TYR 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 7 SER 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: 0.8980 chunk 136 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 0.0570 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.152212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135119 restraints weight = 22878.621| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.35 r_work: 0.3573 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3053 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= 0.124 Angle : 0.567 6.042 26532 Z= 0.299 Chirality : 0.046 0.148 2856 Planarity : 0.004 0.030 3400 Dihedral : 4.963 29.170 2728 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 2.65 % Allowed : 17.05 % Favored : 80.30 % 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 aren not related in a simple way. whole: 0.59 (0.18), residues: 2432 helix: -0.95 (0.79), residues: 28 sheet: 0.90 (0.17), residues: 904 loop : 0.18 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.011 0.001 TYR L 96 PHE 0.013 0.002 PHE B 422 TRP 0.016 0.001 TRP A 178 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00297 (19432) covalent geometry : angle 0.56031 (26440) SS BOND : bond 0.00327 ( 40) SS BOND : angle 1.58996 ( 80) hydrogen bonds : bond 0.03202 ( 672) hydrogen bonds : angle 6.33955 ( 1692) link_NAG-ASN : bond 0.00022 ( 4) link_NAG-ASN : angle 1.13763 ( 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 268 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7512 (p90) REVERT: B 155 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7517 (p90) REVERT: C 155 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7520 (p90) REVERT: D 155 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7513 (p90) outliers start: 56 outliers final: 48 residues processed: 256 average time/residue: 0.1172 time to fit residues: 49.4899 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 : 0.481 ------------------------------------------------------------------------------- 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 155 TYR Chi-restraints excluded: chain A residue 230 CYS 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 L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL 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 155 TYR Chi-restraints excluded: chain B residue 230 CYS 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 I residue 72 THR Chi-restraints excluded: chain E residue 2 VAL 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 155 TYR Chi-restraints excluded: chain C residue 230 CYS 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 J residue 72 THR Chi-restraints excluded: chain F residue 2 VAL 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 155 TYR Chi-restraints excluded: chain D residue 230 CYS 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 K residue 72 THR Chi-restraints excluded: chain G residue 2 VAL 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: 7.9990 chunk 105 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3813 r_free = 0.3813 target = 0.149668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132452 restraints weight = 23134.750| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.37 r_work: 0.3543 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19476 Z= 0.167 Angle : 0.598 5.953 26532 Z= 0.315 Chirality : 0.048 0.166 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.107 37.448 2728 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.11 % 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 aren not related in a simple way. whole: 0.47 (0.17), residues: 2432 helix: -0.82 (0.80), residues: 28 sheet: 0.74 (0.17), residues: 932 loop : 0.13 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.013 0.001 TYR L 96 PHE 0.014 0.002 PHE E 78 TRP 0.011 0.002 TRP C 178 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00408 (19432) covalent geometry : angle 0.58863 (26440) SS BOND : bond 0.00639 ( 40) SS BOND : angle 1.97884 ( 80) hydrogen bonds : bond 0.03312 ( 672) hydrogen bonds : angle 6.41017 ( 1692) link_NAG-ASN : bond 0.00040 ( 4) link_NAG-ASN : angle 1.14227 ( 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 264 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7539 (p90) REVERT: B 155 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7536 (p90) REVERT: C 155 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7544 (p90) REVERT: D 155 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7535 (p90) outliers start: 60 outliers final: 52 residues processed: 248 average time/residue: 0.1111 time to fit residues: 45.0384 Evaluate side-chains 256 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 155 TYR 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 4 MET Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER 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 155 TYR 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 4 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER 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 155 TYR 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 4 MET Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER 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 155 TYR 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 4 MET Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 7 SER 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: 2.9990 chunk 136 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 112 optimal weight: 0.0010 chunk 144 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 148 optimal weight: 0.1980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3858 r_free = 0.3858 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136562 restraints weight = 23043.868| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.36 r_work: 0.3594 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3166 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= 0.117 Angle : 0.558 6.402 26532 Z= 0.294 Chirality : 0.046 0.152 2856 Planarity : 0.004 0.029 3400 Dihedral : 4.930 35.868 2728 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 2.65 % Allowed : 17.23 % Favored : 80.11 % 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 aren not related in a simple way. whole: 0.59 (0.18), residues: 2432 helix: -0.74 (0.74), residues: 28 sheet: 0.85 (0.17), residues: 976 loop : 0.17 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.011 0.001 TYR L 96 PHE 0.013 0.002 PHE B 422 TRP 0.017 0.001 TRP A 178 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00282 (19432) covalent geometry : angle 0.55050 (26440) SS BOND : bond 0.00461 ( 40) SS BOND : angle 1.74029 ( 80) hydrogen bonds : bond 0.03093 ( 672) hydrogen bonds : angle 6.22669 ( 1692) link_NAG-ASN : bond 0.00034 ( 4) link_NAG-ASN : angle 1.12541 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.49 seconds wall clock time: 78 minutes 22.30 seconds (4702.30 seconds total)