Starting phenix.real_space_refine on Thu Jun 4 07:26:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564.map" model { file = "/net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w23_65564/06_2026/9w23_65564_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 94 5.16 5 C 6984 2.51 5 N 1902 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11118 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "a" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {'GU6': 1, 'Z9K': 1, 'Z9L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {'GU6': 1, 'Z9K': 1, 'Z9L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.25, per 1000 atoms: 0.29 Number of scatterers: 11118 At special positions: 0 Unit cell: (108.702, 120.109, 87.901, 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 94 16.00 O 2138 8.00 N 1902 7.00 C 6984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 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 ?1-4 " Z9L C 1 " - " Z9K C 2 " " Z9L D 1 " - " Z9K D 2 " ALPHA1-4 " Z9K C 2 " - " GU6 C 3 " " Z9K D 2 " - " GU6 D 3 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 550.1 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 22 sheets defined 18.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.529A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.623A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.556A pdb=" N TYR A 256 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.617A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 removed outlier: 3.808A pdb=" N SER a 44 " --> pdb=" O SER a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.600A pdb=" N HIS a 229 " --> pdb=" O PRO a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.538A pdb=" N TYR a 256 " --> pdb=" O GLN a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.897A pdb=" N LEU a 345 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 52 Processing helix chain 'b' and resid 61 through 82 Proline residue: b 73 - end of helix Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.685A pdb=" N HIS b 229 " --> pdb=" O PRO b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 252 through 256 Processing helix chain 'b' and resid 341 through 345 removed outlier: 3.607A pdb=" N LEU b 345 " --> pdb=" O GLU b 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.577A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 82 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.624A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.583A pdb=" N TYR B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.470A pdb=" N HIS B 269 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 271 " --> pdb=" O TRP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.630A pdb=" N ASN B 344 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.717A pdb=" N LEU A 169 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.837A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.305A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.263A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 185 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER a 185 " --> pdb=" O ALA a 196 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY a 328 " --> pdb=" O GLY a 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.496A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.671A pdb=" N ILE b 19 " --> pdb=" O GLU b 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.957A pdb=" N LEU a 169 " --> pdb=" O GLN a 35 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN a 166 " --> pdb=" O GLY a 159 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP a 157 " --> pdb=" O TRP a 168 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS a 170 " --> pdb=" O VAL a 155 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL a 155 " --> pdb=" O LYS a 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 56 through 57 removed outlier: 6.944A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.750A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'a' and resid 285 through 287 Processing sheet with id=AB4, first strand: chain 'b' and resid 33 through 36 removed outlier: 3.833A pdb=" N LYS b 33 " --> pdb=" O THR b 165 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU b 169 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP b 157 " --> pdb=" O TRP b 168 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS b 170 " --> pdb=" O VAL b 155 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL b 155 " --> pdb=" O LYS b 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 56 through 58 removed outlier: 6.940A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.636A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 273 through 276 removed outlier: 5.451A pdb=" N ILE b 212 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 185 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 285 through 287 Processing sheet with id=AB9, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.555A pdb=" N LYS B 14 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.635A pdb=" N ILE B 167 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 169 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 157 " --> pdb=" O TRP B 168 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS B 170 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 155 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.868A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.689A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.486A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 678 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: 1.65 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3576 1.34 - 1.46: 2748 1.46 - 1.58: 4931 1.58 - 1.70: 31 1.70 - 1.82: 116 Bond restraints: 11402 Sorted by residual: bond pdb=" C2 Z9K C 2 " pdb=" C3 Z9K C 2 " ideal model delta sigma weight residual 1.523 1.657 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" O9 Z9L C 1 " pdb=" S2 Z9L C 1 " ideal model delta sigma weight residual 1.456 1.583 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" O9 Z9L D 1 " pdb=" S2 Z9L D 1 " ideal model delta sigma weight residual 1.456 1.583 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O19 GU6 C 3 " pdb=" S6 GU6 C 3 " ideal model delta sigma weight residual 1.460 1.580 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" O19 GU6 D 3 " pdb=" S6 GU6 D 3 " ideal model delta sigma weight residual 1.460 1.579 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 11397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 15414 4.40 - 8.80: 43 8.80 - 13.20: 15 13.20 - 17.60: 9 17.60 - 22.00: 5 Bond angle restraints: 15486 Sorted by residual: angle pdb=" C6 Z9L D 1 " pdb=" O6 Z9L D 1 " pdb=" S1 Z9L D 1 " ideal model delta sigma weight residual 117.62 139.62 -22.00 3.00e+00 1.11e-01 5.38e+01 angle pdb=" C6 Z9L C 1 " pdb=" O6 Z9L C 1 " pdb=" S1 Z9L C 1 " ideal model delta sigma weight residual 117.62 139.60 -21.98 3.00e+00 1.11e-01 5.37e+01 angle pdb=" C3 GU6 C 3 " pdb=" O3 GU6 C 3 " pdb=" S3 GU6 C 3 " ideal model delta sigma weight residual 119.53 140.59 -21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C3 GU6 D 3 " pdb=" O3 GU6 D 3 " pdb=" S3 GU6 D 3 " ideal model delta sigma weight residual 119.53 138.81 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O11 Z9L D 1 " pdb=" S1 Z9L D 1 " pdb=" O6 Z9L D 1 " ideal model delta sigma weight residual 105.55 123.20 -17.65 3.00e+00 1.11e-01 3.46e+01 ... (remaining 15481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.51: 6417 30.51 - 61.02: 391 61.02 - 91.52: 44 91.52 - 122.03: 71 122.03 - 152.54: 4 Dihedral angle restraints: 6927 sinusoidal: 2963 harmonic: 3964 Sorted by residual: dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sinusoidal sigma weight residual -86.00 -12.09 -73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -153.35 67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 6924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1505 0.067 - 0.133: 155 0.133 - 0.200: 3 0.200 - 0.266: 8 0.266 - 0.333: 3 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C1 GU6 C 3 " pdb=" O4 Z9K C 2 " pdb=" C2 GU6 C 3 " pdb=" O5 GU6 C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.20e+01 chirality pdb=" C1 GU6 D 3 " pdb=" O4 Z9K D 2 " pdb=" C2 GU6 D 3 " pdb=" O5 GU6 D 3 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.50e+00 chirality pdb=" C2 Z9K C 2 " pdb=" C1 Z9K C 2 " pdb=" C3 Z9K C 2 " pdb=" O2 Z9K C 2 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1671 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ASP a 208 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.016 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 208 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASP B 208 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 208 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 209 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 190 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C ASP B 190 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP B 190 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 191 " 0.009 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 221 2.64 - 3.21: 10141 3.21 - 3.77: 14991 3.77 - 4.34: 21840 4.34 - 4.90: 37563 Nonbonded interactions: 84756 Sorted by model distance: nonbonded pdb=" OD1 ASP A 190 " pdb=" N ASN A 191 " model vdw 2.080 3.120 nonbonded pdb=" N GLU b 281 " pdb=" OE1 GLU b 281 " model vdw 2.124 3.120 nonbonded pdb=" O SER A 233 " pdb=" OG SER A 233 " model vdw 2.164 3.040 nonbonded pdb=" O ASP a 208 " pdb=" OD1 ASP a 208 " model vdw 2.166 3.040 nonbonded pdb=" O TRP A 68 " pdb=" OG1 THR A 72 " model vdw 2.195 3.040 ... (remaining 84751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 352) selection = (chain 'a' and resid 17 through 352) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.007 0.134 11427 Z= 0.328 Angle : 0.874 21.999 15540 Z= 0.344 Chirality : 0.044 0.333 1674 Planarity : 0.002 0.034 1946 Dihedral : 23.132 152.540 4304 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.15 % Allowed : 31.04 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1368 helix: 3.20 (0.44), residues: 154 sheet: -1.08 (0.31), residues: 334 loop : -1.22 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 174 TYR 0.006 0.001 TYR A 323 PHE 0.006 0.001 PHE a 279 TRP 0.006 0.001 TRP a 330 HIS 0.002 0.000 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.33 (11402) covalent geometry : angle 0.85589 / 0.34 (15486) SS BOND : bond 0.00171 / 0.12 ( 21) SS BOND : angle 0.66967 / 0.49 ( 42) hydrogen bonds : bond 0.20836 / 13.12 ( 261) hydrogen bonds : angle 7.48484 / 5.34 ( 678) glycosidic custom : bond 0.02203 / 1.13 ( 2) glycosidic custom : angle 7.01812 / 3.17 ( 6) link_ALPHA1-4 : bond 0.02538 / 1.27 ( 2) link_ALPHA1-4 : angle 6.04201 / 2.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8560 (mt) cc_final: 0.8057 (mp) REVERT: b 47 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8358 (tm-30) REVERT: b 48 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8621 (tmmt) REVERT: B 97 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: B 167 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8931 (mm) outliers start: 38 outliers final: 33 residues processed: 115 average time/residue: 0.1064 time to fit residues: 17.9161 Evaluate side-chains 118 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 78 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 48 LYS Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 318 LEU Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 329 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 82 ASN a 82 ASN ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 82 ASN ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.064508 restraints weight = 20568.036| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.49 r_work: 0.2658 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11427 Z= 0.123 Angle : 0.653 9.058 15540 Z= 0.310 Chirality : 0.049 0.411 1674 Planarity : 0.003 0.033 1946 Dihedral : 22.568 132.963 1689 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.06 % Allowed : 27.98 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.24), residues: 1368 helix: 2.91 (0.42), residues: 156 sheet: -1.14 (0.30), residues: 358 loop : -1.09 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 174 TYR 0.010 0.001 TYR b 113 PHE 0.011 0.001 PHE B 20 TRP 0.007 0.001 TRP A 225 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11402) covalent geometry : angle 0.64587 / 0.31 (15486) SS BOND : bond 0.00188 / 0.13 ( 21) SS BOND : angle 0.83958 / 0.59 ( 42) hydrogen bonds : bond 0.04218 / 2.72 ( 261) hydrogen bonds : angle 5.45590 / 3.87 ( 678) glycosidic custom : bond 0.00495 / 0.26 ( 2) glycosidic custom : angle 4.04010 / 2.04 ( 6) link_ALPHA1-4 : bond 0.01584 / 0.82 ( 2) link_ALPHA1-4 : angle 2.33716 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 35 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: A 97 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8134 (mmm) REVERT: A 345 LEU cc_start: 0.8428 (mt) cc_final: 0.7759 (mp) REVERT: a 97 MET cc_start: 0.8905 (mmm) cc_final: 0.8604 (mmm) REVERT: b 47 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8102 (tm-30) REVERT: b 48 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8585 (tppp) REVERT: b 123 MET cc_start: 0.8878 (mpp) cc_final: 0.8662 (ppp) REVERT: b 276 ASP cc_start: 0.8378 (t0) cc_final: 0.7695 (p0) REVERT: b 324 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: B 71 ILE cc_start: 0.8812 (mm) cc_final: 0.8584 (tp) outliers start: 37 outliers final: 17 residues processed: 115 average time/residue: 0.0964 time to fit residues: 16.3635 Evaluate side-chains 105 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 48 LYS Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 331 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN b 82 ASN ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.063430 restraints weight = 20938.114| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.52 r_work: 0.2635 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11427 Z= 0.168 Angle : 0.638 9.833 15540 Z= 0.300 Chirality : 0.048 0.448 1674 Planarity : 0.003 0.030 1946 Dihedral : 20.756 129.375 1645 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.73 % Allowed : 25.83 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1368 helix: 2.86 (0.42), residues: 156 sheet: -1.18 (0.29), residues: 360 loop : -1.18 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 174 TYR 0.011 0.001 TYR A 113 PHE 0.010 0.001 PHE B 20 TRP 0.008 0.001 TRP a 330 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (11402) covalent geometry : angle 0.63217 / 0.30 (15486) SS BOND : bond 0.00199 / 0.13 ( 21) SS BOND : angle 0.81711 / 0.57 ( 42) hydrogen bonds : bond 0.04138 / 2.64 ( 261) hydrogen bonds : angle 5.19546 / 3.69 ( 678) glycosidic custom : bond 0.00594 / 0.31 ( 2) glycosidic custom : angle 3.75391 / 1.86 ( 6) link_ALPHA1-4 : bond 0.01159 / 0.60 ( 2) link_ALPHA1-4 : angle 1.94390 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 87 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7649 (mm110) REVERT: A 97 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: A 345 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7728 (mp) REVERT: b 31 GLN cc_start: 0.8251 (tp40) cc_final: 0.7985 (mm110) REVERT: b 47 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8102 (tm-30) REVERT: b 48 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8595 (tppp) REVERT: b 276 ASP cc_start: 0.8391 (t0) cc_final: 0.7676 (p0) REVERT: b 324 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: B 71 ILE cc_start: 0.8847 (mm) cc_final: 0.8624 (tp) outliers start: 45 outliers final: 27 residues processed: 122 average time/residue: 0.1060 time to fit residues: 18.7586 Evaluate side-chains 114 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 48 LYS Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 331 TYR Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 309 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 35 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 82 ASN B 107 GLN B 129 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.063589 restraints weight = 21112.504| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.52 r_work: 0.2639 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11427 Z= 0.164 Angle : 0.627 10.799 15540 Z= 0.296 Chirality : 0.050 0.510 1674 Planarity : 0.003 0.036 1946 Dihedral : 18.509 128.914 1643 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.97 % Allowed : 25.41 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.23), residues: 1368 helix: 2.73 (0.42), residues: 156 sheet: -1.16 (0.29), residues: 360 loop : -1.20 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 174 TYR 0.011 0.001 TYR A 113 PHE 0.011 0.001 PHE B 20 TRP 0.008 0.001 TRP a 330 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (11402) covalent geometry : angle 0.62272 / 0.30 (15486) SS BOND : bond 0.00192 / 0.13 ( 21) SS BOND : angle 0.79362 / 0.55 ( 42) hydrogen bonds : bond 0.03928 / 2.53 ( 261) hydrogen bonds : angle 5.04139 / 3.57 ( 678) glycosidic custom : bond 0.00730 / 0.37 ( 2) glycosidic custom : angle 3.28223 / 1.59 ( 6) link_ALPHA1-4 : bond 0.01275 / 0.62 ( 2) link_ALPHA1-4 : angle 1.51334 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: A 345 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7827 (mp) REVERT: a 35 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8712 (tp40) REVERT: b 31 GLN cc_start: 0.8292 (tp40) cc_final: 0.8021 (mm110) REVERT: b 47 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8081 (tm-30) REVERT: b 48 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (tppp) REVERT: b 82 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7698 (m110) REVERT: b 276 ASP cc_start: 0.8391 (t0) cc_final: 0.7688 (p0) REVERT: b 324 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7675 (ttp-170) REVERT: B 71 ILE cc_start: 0.8813 (mm) cc_final: 0.8599 (tp) REVERT: B 175 GLN cc_start: 0.9367 (pm20) cc_final: 0.9130 (pm20) outliers start: 48 outliers final: 32 residues processed: 123 average time/residue: 0.1020 time to fit residues: 18.4827 Evaluate side-chains 121 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 48 LYS Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 331 TYR Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 82 ASN b 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.064974 restraints weight = 20800.199| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.41 r_work: 0.2672 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11427 Z= 0.120 Angle : 0.595 9.062 15540 Z= 0.284 Chirality : 0.048 0.476 1674 Planarity : 0.003 0.030 1946 Dihedral : 17.047 128.025 1641 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.14 % Allowed : 25.33 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.23), residues: 1368 helix: 2.74 (0.42), residues: 156 sheet: -1.12 (0.29), residues: 360 loop : -1.14 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.011 0.001 TYR A 113 PHE 0.011 0.001 PHE a 20 TRP 0.006 0.001 TRP A 225 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11402) covalent geometry : angle 0.59213 / 0.28 (15486) SS BOND : bond 0.00164 / 0.12 ( 21) SS BOND : angle 0.68443 / 0.48 ( 42) hydrogen bonds : bond 0.03576 / 2.30 ( 261) hydrogen bonds : angle 4.90514 / 3.47 ( 678) glycosidic custom : bond 0.01105 / 0.58 ( 2) glycosidic custom : angle 2.66366 / 1.30 ( 6) link_ALPHA1-4 : bond 0.01440 / 0.72 ( 2) link_ALPHA1-4 : angle 1.74747 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7424 (mm-40) REVERT: A 345 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7751 (mp) REVERT: b 31 GLN cc_start: 0.8324 (tp40) cc_final: 0.8059 (mm110) REVERT: b 47 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8046 (tm-30) REVERT: b 48 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (tppp) REVERT: b 82 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7837 (m110) REVERT: b 276 ASP cc_start: 0.8357 (t0) cc_final: 0.7711 (p0) REVERT: b 324 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7594 (ttp-170) REVERT: B 175 GLN cc_start: 0.9346 (pm20) cc_final: 0.9083 (pm20) outliers start: 50 outliers final: 36 residues processed: 126 average time/residue: 0.0980 time to fit residues: 18.2685 Evaluate side-chains 123 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 48 LYS Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 331 TYR Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 4 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 35 GLN b 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.064319 restraints weight = 21196.531| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.53 r_work: 0.2654 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11427 Z= 0.143 Angle : 0.600 9.707 15540 Z= 0.286 Chirality : 0.046 0.434 1674 Planarity : 0.003 0.048 1946 Dihedral : 16.608 128.876 1641 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.47 % Allowed : 24.92 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1368 helix: 2.73 (0.42), residues: 156 sheet: -1.12 (0.29), residues: 360 loop : -1.15 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 174 TYR 0.009 0.001 TYR A 113 PHE 0.011 0.001 PHE B 20 TRP 0.011 0.001 TRP B 118 HIS 0.003 0.001 HIS a 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11402) covalent geometry : angle 0.59618 / 0.29 (15486) SS BOND : bond 0.00250 / 0.19 ( 21) SS BOND : angle 0.76613 / 0.55 ( 42) hydrogen bonds : bond 0.03570 / 2.30 ( 261) hydrogen bonds : angle 4.87845 / 3.44 ( 678) glycosidic custom : bond 0.00605 / 0.31 ( 2) glycosidic custom : angle 2.58279 / 1.28 ( 6) link_ALPHA1-4 : bond 0.01416 / 0.71 ( 2) link_ALPHA1-4 : angle 1.69494 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 85 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 97 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: A 345 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7722 (mp) REVERT: a 35 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8687 (tp40) REVERT: b 31 GLN cc_start: 0.8321 (tp40) cc_final: 0.8051 (mm110) REVERT: b 47 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8097 (tm-30) REVERT: b 82 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7937 (m110) REVERT: b 276 ASP cc_start: 0.8363 (t0) cc_final: 0.7709 (p0) REVERT: b 324 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: B 123 MET cc_start: 0.7505 (mmm) cc_final: 0.7172 (mmm) REVERT: B 175 GLN cc_start: 0.9338 (pm20) cc_final: 0.9056 (pm20) outliers start: 54 outliers final: 41 residues processed: 128 average time/residue: 0.0994 time to fit residues: 18.8181 Evaluate side-chains 128 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 331 TYR Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0000 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 0.0970 chunk 114 optimal weight: 0.0570 chunk 90 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN b 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.066649 restraints weight = 20873.630| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.53 r_work: 0.2708 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11427 Z= 0.095 Angle : 0.580 10.709 15540 Z= 0.276 Chirality : 0.045 0.367 1674 Planarity : 0.003 0.031 1946 Dihedral : 15.945 126.299 1637 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.15 % Allowed : 26.32 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1368 helix: 2.67 (0.42), residues: 156 sheet: -1.03 (0.30), residues: 360 loop : -1.06 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.007 0.001 TYR A 113 PHE 0.011 0.001 PHE B 20 TRP 0.009 0.001 TRP B 118 HIS 0.003 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (11402) covalent geometry : angle 0.57770 / 0.28 (15486) SS BOND : bond 0.00157 / 0.12 ( 21) SS BOND : angle 0.61667 / 0.44 ( 42) hydrogen bonds : bond 0.03070 / 2.01 ( 261) hydrogen bonds : angle 4.71462 / 3.31 ( 678) glycosidic custom : bond 0.00496 / 0.26 ( 2) glycosidic custom : angle 2.18537 / 1.04 ( 6) link_ALPHA1-4 : bond 0.01443 / 0.72 ( 2) link_ALPHA1-4 : angle 1.66080 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7433 (mm-40) REVERT: A 97 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: A 345 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7698 (mp) REVERT: a 35 GLN cc_start: 0.8991 (tp40) cc_final: 0.8638 (tp40) REVERT: a 97 MET cc_start: 0.8939 (mmm) cc_final: 0.8667 (mmm) REVERT: a 323 TYR cc_start: 0.8856 (m-80) cc_final: 0.8594 (m-80) REVERT: b 31 GLN cc_start: 0.8318 (tp40) cc_final: 0.8055 (mm110) REVERT: b 47 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8058 (tm-30) REVERT: b 82 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7917 (m110) REVERT: b 276 ASP cc_start: 0.8251 (t0) cc_final: 0.7649 (p0) REVERT: b 324 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: B 175 GLN cc_start: 0.9325 (pm20) cc_final: 0.9034 (pm20) outliers start: 38 outliers final: 28 residues processed: 117 average time/residue: 0.1057 time to fit residues: 18.1407 Evaluate side-chains 114 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN b 82 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065473 restraints weight = 21026.316| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.52 r_work: 0.2683 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11427 Z= 0.129 Angle : 0.597 11.290 15540 Z= 0.282 Chirality : 0.044 0.314 1674 Planarity : 0.003 0.053 1946 Dihedral : 15.454 124.160 1637 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.64 % Allowed : 26.08 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1368 helix: 2.67 (0.42), residues: 156 sheet: -1.16 (0.29), residues: 370 loop : -1.04 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 174 TYR 0.011 0.001 TYR B 323 PHE 0.011 0.001 PHE B 20 TRP 0.007 0.001 TRP B 118 HIS 0.003 0.001 HIS a 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11402) covalent geometry : angle 0.59528 / 0.28 (15486) SS BOND : bond 0.00152 / 0.11 ( 21) SS BOND : angle 0.67888 / 0.48 ( 42) hydrogen bonds : bond 0.03279 / 2.12 ( 261) hydrogen bonds : angle 4.71887 / 3.31 ( 678) glycosidic custom : bond 0.00423 / 0.22 ( 2) glycosidic custom : angle 1.93820 / 0.89 ( 6) link_ALPHA1-4 : bond 0.01440 / 0.72 ( 2) link_ALPHA1-4 : angle 1.72693 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7659 (mm-40) REVERT: A 97 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8067 (mmm) REVERT: A 345 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7766 (mp) REVERT: a 35 GLN cc_start: 0.9023 (tp40) cc_final: 0.8614 (tp40) REVERT: b 31 GLN cc_start: 0.8325 (tp40) cc_final: 0.8055 (mm110) REVERT: b 47 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8059 (tm-30) REVERT: b 82 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7892 (m110) REVERT: b 276 ASP cc_start: 0.8275 (t0) cc_final: 0.7657 (p0) REVERT: b 324 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: B 175 GLN cc_start: 0.9318 (pm20) cc_final: 0.9019 (pm20) outliers start: 44 outliers final: 35 residues processed: 115 average time/residue: 0.1000 time to fit residues: 17.1578 Evaluate side-chains 118 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 35 GLN b 82 ASN ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.063266 restraints weight = 21036.346| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.51 r_work: 0.2632 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11427 Z= 0.219 Angle : 0.637 9.365 15540 Z= 0.309 Chirality : 0.045 0.311 1674 Planarity : 0.003 0.031 1946 Dihedral : 15.054 121.817 1637 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.81 % Allowed : 25.99 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1368 helix: 2.65 (0.42), residues: 156 sheet: -1.22 (0.29), residues: 370 loop : -1.16 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.013 0.001 TYR B 323 PHE 0.012 0.001 PHE B 20 TRP 0.011 0.001 TRP a 311 HIS 0.004 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (11402) covalent geometry : angle 0.62872 / 0.31 (15486) SS BOND : bond 0.00217 / 0.14 ( 21) SS BOND : angle 0.88439 / 0.62 ( 42) hydrogen bonds : bond 0.03907 / 2.49 ( 261) hydrogen bonds : angle 4.93280 / 3.47 ( 678) glycosidic custom : bond 0.00503 / 0.25 ( 2) glycosidic custom : angle 4.67656 / 2.57 ( 6) link_ALPHA1-4 : bond 0.01506 / 0.75 ( 2) link_ALPHA1-4 : angle 1.84502 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7725 (mm-40) REVERT: A 35 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7771 (mp-120) REVERT: A 97 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8111 (mmm) REVERT: A 345 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7916 (mp) REVERT: a 35 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8711 (tp40) REVERT: b 31 GLN cc_start: 0.8391 (tp40) cc_final: 0.8101 (mm110) REVERT: b 47 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8103 (tm-30) REVERT: b 276 ASP cc_start: 0.8394 (t0) cc_final: 0.7701 (p0) REVERT: b 324 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7709 (ttp-170) outliers start: 46 outliers final: 36 residues processed: 118 average time/residue: 0.0996 time to fit residues: 17.3282 Evaluate side-chains 123 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 309 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 35 GLN b 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.064332 restraints weight = 21089.040| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.55 r_work: 0.2653 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11427 Z= 0.132 Angle : 0.603 9.430 15540 Z= 0.290 Chirality : 0.044 0.315 1674 Planarity : 0.003 0.063 1946 Dihedral : 14.797 119.644 1637 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.15 % Allowed : 26.66 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.23), residues: 1368 helix: 2.64 (0.42), residues: 156 sheet: -1.22 (0.29), residues: 370 loop : -1.13 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 174 TYR 0.011 0.001 TYR B 323 PHE 0.011 0.001 PHE a 20 TRP 0.007 0.001 TRP A 115 HIS 0.004 0.001 HIS a 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (11402) covalent geometry : angle 0.59776 / 0.29 (15486) SS BOND : bond 0.00171 / 0.12 ( 21) SS BOND : angle 0.71869 / 0.51 ( 42) hydrogen bonds : bond 0.03508 / 2.27 ( 261) hydrogen bonds : angle 4.87100 / 3.43 ( 678) glycosidic custom : bond 0.00426 / 0.22 ( 2) glycosidic custom : angle 3.74571 / 2.03 ( 6) link_ALPHA1-4 : bond 0.01573 / 0.78 ( 2) link_ALPHA1-4 : angle 1.61402 / 0.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7698 (mm-40) REVERT: A 35 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7721 (mp-120) REVERT: A 97 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8109 (mmm) REVERT: A 345 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7801 (mp) REVERT: a 35 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8731 (tp40) REVERT: b 31 GLN cc_start: 0.8339 (tp40) cc_final: 0.8054 (mm110) REVERT: b 47 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8094 (tm-30) REVERT: b 82 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8113 (m110) REVERT: b 123 MET cc_start: 0.8922 (mpp) cc_final: 0.8648 (mpp) REVERT: b 276 ASP cc_start: 0.8363 (t0) cc_final: 0.7700 (p0) REVERT: b 324 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7676 (ttp-170) REVERT: B 123 MET cc_start: 0.7380 (mmm) cc_final: 0.7109 (mmm) outliers start: 38 outliers final: 31 residues processed: 111 average time/residue: 0.1035 time to fit residues: 17.1486 Evaluate side-chains 119 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 71 ILE Chi-restraints excluded: chain a residue 89 MET Chi-restraints excluded: chain a residue 113 TYR Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain b residue 19 ILE Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 324 ARG Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 309 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 0.7980 chunk 134 optimal weight: 0.0270 chunk 41 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 35 GLN a 263 GLN b 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.065059 restraints weight = 21067.687| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.45 r_work: 0.2674 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11427 Z= 0.121 Angle : 0.594 9.057 15540 Z= 0.285 Chirality : 0.044 0.318 1674 Planarity : 0.003 0.032 1946 Dihedral : 14.572 117.681 1637 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.31 % Allowed : 26.41 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1368 helix: 2.62 (0.42), residues: 156 sheet: -1.22 (0.29), residues: 370 loop : -1.10 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.010 0.001 TYR B 323 PHE 0.011 0.001 PHE a 20 TRP 0.007 0.001 TRP A 115 HIS 0.003 0.001 HIS a 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (11402) covalent geometry : angle 0.58926 / 0.28 (15486) SS BOND : bond 0.00162 / 0.11 ( 21) SS BOND : angle 0.68436 / 0.49 ( 42) hydrogen bonds : bond 0.03371 / 2.18 ( 261) hydrogen bonds : angle 4.82646 / 3.40 ( 678) glycosidic custom : bond 0.00399 / 0.21 ( 2) glycosidic custom : angle 3.37493 / 1.81 ( 6) link_ALPHA1-4 : bond 0.01459 / 0.73 ( 2) link_ALPHA1-4 : angle 1.58304 / 0.86 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.36 seconds wall clock time: 51 minutes 13.14 seconds (3073.14 seconds total)