Starting phenix.real_space_refine on Sat Oct 24 10:30:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbt_52029/10_2026/9hbt_52029.map" } resolution = 3.46 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= 0.009 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 85 5.16 5 C 8198 2.51 5 N 2400 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13327 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2452 Chain: "O" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2452 Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 2414 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2403 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 314, 2403 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2432 Chain: "Q" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2452 Chain: "R" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 2429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2418 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 316, 2418 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2448 Chain: "S" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 198 " occ=0.40 residue: pdb=" N AARG B 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG B 198 " occ=0.40 residue: pdb=" N AARG C 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG C 198 " occ=0.40 residue: pdb=" N AARG D 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG D 198 " occ=0.40 residue: pdb=" N AARG E 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG E 198 " occ=0.40 Time building chain proxies: 4.69, per 1000 atoms: 0.35 Number of scatterers: 13327 At special positions: 0 Unit cell: (118.368, 126.588, 76.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 60 15.00 O 2584 8.00 N 2400 7.00 C 8198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 995.3 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 15 sheets defined 52.1% alpha, 7.0% beta 0 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.628A pdb=" N VAL A 128 " --> pdb=" O CYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 143 through 173 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.819A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.648A pdb=" N ASN A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 58 through 74 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.540A pdb=" N VAL B 128 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 143 through 175 removed outlier: 4.293A pdb=" N VAL B 174 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.178A pdb=" N GLY B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.670A pdb=" N VAL C 128 " --> pdb=" O CYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 175 removed outlier: 4.383A pdb=" N VAL C 174 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.715A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 307 through 312 Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 58 through 74 Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 119 through 128 removed outlier: 3.590A pdb=" N VAL E 128 " --> pdb=" O CYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 143 through 173 Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.905A pdb=" N ALA E 209 " --> pdb=" O GLY E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 307 through 312 removed outlier: 4.107A pdb=" N GLY E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 340 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 9.448A pdb=" N SER A 271 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N SER A 278 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 273 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 273 removed outlier: 9.506A pdb=" N SER B 271 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N SER B 278 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 273 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA7, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AA8, first strand: chain 'C' and resid 270 through 273 removed outlier: 3.941A pdb=" N SER C 273 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE C 279 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB1, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'D' and resid 270 through 273 removed outlier: 8.628A pdb=" N SER D 271 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N SER D 278 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 273 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'E' and resid 270 through 273 removed outlier: 9.031A pdb=" N SER E 271 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER E 278 " --> pdb=" O SER E 271 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER E 273 " --> pdb=" O ASP E 276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 284 through 286 567 hydrogen bonds defined for protein. 1625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4201 1.34 - 1.46: 2301 1.46 - 1.57: 6959 1.57 - 1.69: 115 1.69 - 1.81: 115 Bond restraints: 13691 Sorted by residual: bond pdb=" N3 Y5P S 2 " pdb=" C4 Y5P S 2 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" N3 Y5P O 2 " pdb=" C4 Y5P O 2 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N3 Y5P Q 2 " pdb=" C4 Y5P Q 2 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" N3 Y5P P 2 " pdb=" C4 Y5P P 2 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" N3 Y5P R 2 " pdb=" C4 Y5P R 2 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 13686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18287 2.39 - 4.78: 269 4.78 - 7.17: 65 7.17 - 9.56: 35 9.56 - 11.95: 20 Bond angle restraints: 18676 Sorted by residual: angle pdb=" N1 Y5P R 8 " pdb=" C2 Y5P R 8 " pdb=" N3 Y5P R 8 " ideal model delta sigma weight residual 126.68 114.73 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 Y5P Q 12 " pdb=" C2 Y5P Q 12 " pdb=" N3 Y5P Q 12 " ideal model delta sigma weight residual 126.68 114.78 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P P 12 " pdb=" C2 Y5P P 12 " pdb=" N3 Y5P P 12 " ideal model delta sigma weight residual 126.68 114.79 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P P 10 " pdb=" C2 Y5P P 10 " pdb=" N3 Y5P P 10 " ideal model delta sigma weight residual 126.68 114.80 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P Q 8 " pdb=" C2 Y5P Q 8 " pdb=" N3 Y5P Q 8 " ideal model delta sigma weight residual 126.68 114.81 11.87 3.00e+00 1.11e-01 1.57e+01 ... (remaining 18671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 8370 27.64 - 55.29: 595 55.29 - 82.93: 273 82.93 - 110.57: 56 110.57 - 138.21: 4 Dihedral angle restraints: 9298 sinusoidal: 4782 harmonic: 4516 Sorted by residual: dihedral pdb=" P Y5P S 8 " pdb=" O5' Y5P S 8 " pdb=" C5' Y5P S 8 " pdb=" C4' Y5P S 8 " ideal model delta sinusoidal sigma weight residual 248.90 110.69 138.21 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" P Y5P R 8 " pdb=" O5' Y5P R 8 " pdb=" C5' Y5P R 8 " pdb=" C4' Y5P R 8 " ideal model delta sinusoidal sigma weight residual 248.90 114.78 134.12 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" P Y5P Q 8 " pdb=" O5' Y5P Q 8 " pdb=" C5' Y5P Q 8 " pdb=" C4' Y5P Q 8 " ideal model delta sinusoidal sigma weight residual 248.90 115.80 133.10 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 9295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1439 0.027 - 0.055: 458 0.055 - 0.082: 91 0.082 - 0.109: 65 0.109 - 0.136: 39 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE E 230 " pdb=" N ILE E 230 " pdb=" C ILE E 230 " pdb=" CB ILE E 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE D 325 " pdb=" N ILE D 325 " pdb=" C ILE D 325 " pdb=" CB ILE D 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 2089 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 35 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 36 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 35 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO D 36 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' P5P Q 6 " 0.011 2.00e-02 2.50e+03 6.71e-03 1.12e+00 pdb=" N9 P5P Q 6 " -0.018 2.00e-02 2.50e+03 pdb=" C8 P5P Q 6 " 0.001 2.00e-02 2.50e+03 pdb=" N7 P5P Q 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 P5P Q 6 " 0.002 2.00e-02 2.50e+03 pdb=" C6 P5P Q 6 " 0.002 2.00e-02 2.50e+03 pdb=" N1 P5P Q 6 " 0.001 2.00e-02 2.50e+03 pdb=" C2 P5P Q 6 " -0.001 2.00e-02 2.50e+03 pdb=" N3 P5P Q 6 " -0.002 2.00e-02 2.50e+03 pdb=" C4 P5P Q 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 72 2.52 - 3.12: 9941 3.12 - 3.71: 20641 3.71 - 4.31: 28601 4.31 - 4.90: 47649 Nonbonded interactions: 106904 Sorted by model distance: nonbonded pdb=" O LEU A 295 " pdb=" OG SER E 340 " model vdw 1.926 3.040 nonbonded pdb=" OG SER B 340 " pdb=" O LEU C 295 " model vdw 1.935 3.040 nonbonded pdb=" OG SER A 340 " pdb=" O LEU B 295 " model vdw 1.961 3.040 nonbonded pdb=" OG SER C 340 " pdb=" O LEU D 295 " model vdw 1.973 3.040 nonbonded pdb=" OG SER D 340 " pdb=" O LEU E 295 " model vdw 1.993 3.040 ... (remaining 106899 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 197 or resid 199 through 313 or resid 317 throu \ gh 349)) selection = (chain 'B' and (resid 34 through 197 or resid 199 through 313 or resid 317 throu \ gh 349)) selection = (chain 'C' and (resid 34 through 197 or resid 199 through 349)) selection = (chain 'D' and (resid 34 through 197 or resid 199 through 313 or resid 317 throu \ gh 349)) selection = (chain 'E' and (resid 34 through 197 or resid 199 through 313 or resid 317 throu \ gh 349)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.40 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: 2.780 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 : 0.012 0.890 13692 Z= 0.880 Angle : 0.871 11.945 18676 Z= 0.337 Chirality : 0.035 0.136 2092 Planarity : 0.003 0.029 2204 Dihedral : 22.440 138.213 6402 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.81 % Allowed : 17.15 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.23), residues: 1584 helix: 2.33 (0.19), residues: 775 sheet: -1.19 (0.50), residues: 70 loop : 0.65 (0.26), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 158 TYR 0.007 0.001 TYR C 191 PHE 0.007 0.001 PHE D 189 TRP 0.008 0.001 TRP D 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.44 (13691) covalent geometry : angle 0.87115 / 0.34 (18676) hydrogen bonds : bond 0.12942 / 8.49 ( 567) hydrogen bonds : angle 4.66868 / 3.48 ( 1625) Misc. bond : bond 0.89024 / 46.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 365 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 VAL cc_start: 0.8117 (m) cc_final: 0.7874 (p) REVERT: A 252 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: A 263 ASP cc_start: 0.8525 (t70) cc_final: 0.7951 (t0) REVERT: A 311 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5896 (mm-30) REVERT: B 135 MET cc_start: 0.0892 (tpt) cc_final: 0.0610 (tpp) REVERT: B 169 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7598 (mtt180) REVERT: B 178 GLU cc_start: 0.7867 (mp0) cc_final: 0.7628 (mp0) REVERT: C 119 ARG cc_start: 0.6652 (ttp80) cc_final: 0.6216 (ttp80) REVERT: C 121 THR cc_start: 0.7235 (p) cc_final: 0.6767 (m) REVERT: E 38 ASN cc_start: 0.7569 (m-40) cc_final: 0.7229 (p0) outliers start: 32 outliers final: 8 residues processed: 394 average time/residue: 0.1406 time to fit residues: 74.8181 Evaluate side-chains 225 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.227468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181156 restraints weight = 47732.099| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 4.15 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13692 Z= 0.210 Angle : 0.674 7.986 18676 Z= 0.340 Chirality : 0.041 0.172 2092 Planarity : 0.005 0.039 2204 Dihedral : 23.835 143.982 3531 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.12 % Allowed : 20.97 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1584 helix: 1.62 (0.19), residues: 791 sheet: -1.32 (0.51), residues: 68 loop : 0.56 (0.26), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.028 0.002 TYR B 123 PHE 0.016 0.002 PHE D 189 TRP 0.019 0.002 TRP D 259 HIS 0.007 0.001 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (13691) covalent geometry : angle 0.67408 / 0.34 (18676) hydrogen bonds : bond 0.04409 / 2.95 ( 567) hydrogen bonds : angle 4.46489 / 3.33 ( 1625) Misc. bond : bond 0.00240 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8471 (t70) cc_final: 0.8001 (t0) REVERT: B 38 ASN cc_start: 0.7446 (p0) cc_final: 0.7194 (p0) REVERT: B 83 LYS cc_start: 0.5372 (mttt) cc_final: 0.4344 (mttt) REVERT: B 169 ARG cc_start: 0.8150 (mtt180) cc_final: 0.6223 (mtt-85) REVERT: B 311 GLU cc_start: 0.5912 (mm-30) cc_final: 0.5693 (mm-30) REVERT: C 263 ASP cc_start: 0.6203 (t0) cc_final: 0.5714 (t0) REVERT: E 38 ASN cc_start: 0.7740 (m-40) cc_final: 0.7491 (p0) REVERT: E 146 MET cc_start: 0.6580 (mmp) cc_final: 0.6328 (mmp) REVERT: E 158 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6570 (mtt90) outliers start: 37 outliers final: 19 residues processed: 258 average time/residue: 0.1228 time to fit residues: 44.5163 Evaluate side-chains 217 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 158 ARG Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [65, 69, 97, 50, 144, 2, 126, 34, 100, 68, 76] chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 226 GLN B 59 ASN B 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.228671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.181645 restraints weight = 53324.003| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.34 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13692 Z= 0.149 Angle : 0.621 7.716 18676 Z= 0.315 Chirality : 0.039 0.141 2092 Planarity : 0.004 0.042 2204 Dihedral : 23.638 145.931 3521 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.03 % Allowed : 22.84 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.22), residues: 1584 helix: 1.43 (0.19), residues: 791 sheet: -1.18 (0.52), residues: 64 loop : 0.55 (0.26), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 92 TYR 0.029 0.002 TYR A 207 PHE 0.026 0.002 PHE A 54 TRP 0.033 0.002 TRP E 270 HIS 0.005 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (13691) covalent geometry : angle 0.62138 / 0.32 (18676) hydrogen bonds : bond 0.03898 / 2.60 ( 567) hydrogen bonds : angle 4.37882 / 3.24 ( 1625) Misc. bond : bond 0.00125 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.7486 (p0) cc_final: 0.7167 (p0) REVERT: B 83 LYS cc_start: 0.5646 (mttt) cc_final: 0.4668 (mttt) REVERT: B 169 ARG cc_start: 0.8080 (mtt180) cc_final: 0.6442 (mtm180) REVERT: B 311 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5549 (mm-30) REVERT: C 148 GLN cc_start: 0.7263 (tp-100) cc_final: 0.7018 (tp-100) REVERT: C 263 ASP cc_start: 0.6285 (t0) cc_final: 0.5694 (t0) REVERT: D 146 MET cc_start: 0.7009 (tpp) cc_final: 0.6677 (tpp) REVERT: E 38 ASN cc_start: 0.7737 (m-40) cc_final: 0.7529 (p0) REVERT: E 158 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6563 (mtt90) outliers start: 22 outliers final: 16 residues processed: 230 average time/residue: 0.1141 time to fit residues: 37.6416 Evaluate side-chains 217 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain E residue 158 ARG Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [88, 89, 0, 46, 153, 158, 145, 17, 70, 33, 133] chunk 88 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 158 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN C 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.224963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.176324 restraints weight = 44986.343| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 4.27 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13692 Z= 0.256 Angle : 0.712 9.819 18676 Z= 0.357 Chirality : 0.043 0.173 2092 Planarity : 0.005 0.059 2204 Dihedral : 23.650 149.846 3516 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.81 % Allowed : 23.62 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1584 helix: 1.01 (0.19), residues: 780 sheet: -1.78 (0.50), residues: 68 loop : 0.29 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 92 TYR 0.025 0.002 TYR B 123 PHE 0.020 0.002 PHE D 189 TRP 0.057 0.003 TRP E 270 HIS 0.008 0.002 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (13691) covalent geometry : angle 0.71163 / 0.36 (18676) hydrogen bonds : bond 0.04308 / 2.88 ( 567) hydrogen bonds : angle 4.59985 / 3.40 ( 1625) Misc. bond : bond 0.00110 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.7552 (p0) cc_final: 0.7254 (p0) REVERT: B 135 MET cc_start: 0.0566 (tpp) cc_final: 0.0311 (tpp) REVERT: B 311 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5808 (mm-30) REVERT: C 197 TYR cc_start: 0.8456 (t80) cc_final: 0.8193 (t80) REVERT: C 263 ASP cc_start: 0.6363 (t0) cc_final: 0.6056 (t0) REVERT: C 287 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7957 (mp) REVERT: D 146 MET cc_start: 0.7096 (tpp) cc_final: 0.6789 (tpp) REVERT: D 210 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7997 (mtpp) REVERT: E 38 ASN cc_start: 0.7765 (m-40) cc_final: 0.7554 (p0) outliers start: 34 outliers final: 24 residues processed: 236 average time/residue: 0.1123 time to fit residues: 38.3574 Evaluate side-chains 221 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 339 LYS Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [6, 4, 78, 157, 1, 5, 158, 87, 44, 139, 32] chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 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 = 0.4441 r_free = 0.4441 target = 0.227023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.180805 restraints weight = 46563.905| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.93 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13692 Z= 0.171 Angle : 0.645 7.914 18676 Z= 0.324 Chirality : 0.040 0.147 2092 Planarity : 0.004 0.048 2204 Dihedral : 23.516 151.816 3516 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.49 % Allowed : 24.32 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1584 helix: 1.08 (0.19), residues: 780 sheet: -1.85 (0.50), residues: 68 loop : 0.23 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 92 TYR 0.022 0.002 TYR B 123 PHE 0.025 0.002 PHE A 54 TRP 0.028 0.002 TRP E 270 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (13691) covalent geometry : angle 0.64470 / 0.32 (18676) hydrogen bonds : bond 0.03903 / 2.59 ( 567) hydrogen bonds : angle 4.45474 / 3.30 ( 1625) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7037 (tm-30) REVERT: B 38 ASN cc_start: 0.7505 (p0) cc_final: 0.7203 (p0) REVERT: B 169 ARG cc_start: 0.8165 (mtt180) cc_final: 0.6630 (mtm-85) REVERT: B 311 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5891 (mm-30) REVERT: C 197 TYR cc_start: 0.8471 (t80) cc_final: 0.8162 (t80) REVERT: C 263 ASP cc_start: 0.6236 (t0) cc_final: 0.5849 (t0) REVERT: C 287 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (mp) REVERT: D 38 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6579 (p0) REVERT: D 146 MET cc_start: 0.7020 (tpp) cc_final: 0.6744 (tpp) REVERT: D 210 LYS cc_start: 0.8305 (mtpt) cc_final: 0.8096 (mtpp) REVERT: E 38 ASN cc_start: 0.7727 (m-40) cc_final: 0.7515 (p0) outliers start: 30 outliers final: 23 residues processed: 228 average time/residue: 0.1068 time to fit residues: 36.1698 Evaluate side-chains 226 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [107, 138, 49, 78, 36, 12, 145, 158, 18, 50, 147] chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 181 GLN B 59 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.227029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177894 restraints weight = 53158.591| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 4.54 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13692 Z= 0.176 Angle : 0.651 8.689 18676 Z= 0.326 Chirality : 0.041 0.160 2092 Planarity : 0.004 0.047 2204 Dihedral : 23.424 154.172 3515 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.81 % Allowed : 24.71 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1584 helix: 1.05 (0.19), residues: 780 sheet: -1.77 (0.51), residues: 68 loop : 0.18 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 92 TYR 0.024 0.002 TYR B 197 PHE 0.023 0.002 PHE A 54 TRP 0.021 0.002 TRP A 120 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (13691) covalent geometry : angle 0.65085 / 0.33 (18676) hydrogen bonds : bond 0.03873 / 2.58 ( 567) hydrogen bonds : angle 4.46867 / 3.30 ( 1625) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 342 TYR cc_start: 0.7435 (t80) cc_final: 0.7050 (t80) REVERT: B 38 ASN cc_start: 0.7601 (p0) cc_final: 0.7301 (p0) REVERT: B 83 LYS cc_start: 0.5740 (mttt) cc_final: 0.5376 (mttt) REVERT: B 146 MET cc_start: 0.7250 (ppp) cc_final: 0.6717 (tmm) REVERT: B 169 ARG cc_start: 0.8164 (mtt180) cc_final: 0.6598 (mtm-85) REVERT: B 311 GLU cc_start: 0.6297 (mm-30) cc_final: 0.5956 (mm-30) REVERT: C 197 TYR cc_start: 0.8400 (t80) cc_final: 0.8103 (t80) REVERT: C 263 ASP cc_start: 0.6352 (t0) cc_final: 0.5960 (t0) REVERT: D 38 ASN cc_start: 0.7140 (OUTLIER) cc_final: 0.6585 (p0) REVERT: D 146 MET cc_start: 0.7068 (tpp) cc_final: 0.6771 (tpp) REVERT: E 38 ASN cc_start: 0.7754 (m-40) cc_final: 0.7539 (p0) outliers start: 34 outliers final: 29 residues processed: 226 average time/residue: 0.1044 time to fit residues: 35.2653 Evaluate side-chains 219 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 339 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [148, 44, 121, 104, 120, 17, 137, 105, 66, 84, 28] chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 181 GLN B 59 ASN B 75 HIS C 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.229167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180972 restraints weight = 52976.473| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.53 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13692 Z= 0.129 Angle : 0.640 10.668 18676 Z= 0.320 Chirality : 0.039 0.148 2092 Planarity : 0.004 0.054 2204 Dihedral : 23.232 155.326 3515 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.57 % Allowed : 24.63 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1584 helix: 1.14 (0.19), residues: 780 sheet: -1.66 (0.52), residues: 66 loop : 0.19 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 92 TYR 0.025 0.002 TYR E 197 PHE 0.027 0.001 PHE A 54 TRP 0.023 0.001 TRP A 120 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13691) covalent geometry : angle 0.64048 / 0.32 (18676) hydrogen bonds : bond 0.03663 / 2.43 ( 567) hydrogen bonds : angle 4.39476 / 3.27 ( 1625) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.7599 (p0) cc_final: 0.7292 (p0) REVERT: B 83 LYS cc_start: 0.5640 (mttt) cc_final: 0.5350 (mttt) REVERT: B 169 ARG cc_start: 0.8064 (mtt180) cc_final: 0.6488 (mtt-85) REVERT: B 311 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5900 (mm-30) REVERT: C 263 ASP cc_start: 0.5988 (t0) cc_final: 0.5647 (t0) REVERT: D 38 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6617 (p0) REVERT: D 146 MET cc_start: 0.7070 (tpp) cc_final: 0.6785 (tpp) outliers start: 31 outliers final: 28 residues processed: 220 average time/residue: 0.1016 time to fit residues: 33.6609 Evaluate side-chains 225 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [159, 41, 51, 109, 23, 96, 155, 149, 1, 72, 65] chunk 159 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 96 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.4440 r_free = 0.4440 target = 0.226885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181159 restraints weight = 46333.123| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.89 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13692 Z= 0.188 Angle : 0.657 9.094 18676 Z= 0.329 Chirality : 0.041 0.169 2092 Planarity : 0.004 0.056 2204 Dihedral : 23.159 156.628 3515 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.96 % Allowed : 24.08 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1584 helix: 1.01 (0.19), residues: 780 sheet: -1.65 (0.54), residues: 66 loop : 0.14 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 92 TYR 0.040 0.002 TYR A 342 PHE 0.030 0.002 PHE A 54 TRP 0.021 0.002 TRP A 120 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (13691) covalent geometry : angle 0.65719 / 0.33 (18676) hydrogen bonds : bond 0.03846 / 2.57 ( 567) hydrogen bonds : angle 4.46530 / 3.31 ( 1625) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.7536 (p0) cc_final: 0.7238 (p0) REVERT: B 146 MET cc_start: 0.6653 (tmm) cc_final: 0.6442 (tmm) REVERT: B 169 ARG cc_start: 0.8137 (mtt180) cc_final: 0.6309 (mtm180) REVERT: B 311 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5826 (mm-30) REVERT: C 197 TYR cc_start: 0.8492 (t80) cc_final: 0.8207 (t80) REVERT: C 242 LEU cc_start: 0.7992 (tp) cc_final: 0.7771 (tp) REVERT: C 263 ASP cc_start: 0.6319 (t0) cc_final: 0.5955 (t0) REVERT: C 287 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7941 (mp) REVERT: D 38 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6625 (p0) REVERT: D 146 MET cc_start: 0.7115 (tpp) cc_final: 0.6828 (tpp) outliers start: 36 outliers final: 31 residues processed: 222 average time/residue: 0.0963 time to fit residues: 32.6352 Evaluate side-chains 221 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [35, 25, 94, 26, 147, 132, 157, 28, 32, 36, 61] chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.0020 chunk 26 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.7128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.4459 r_free = 0.4459 target = 0.229316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184559 restraints weight = 48790.614| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.92 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13692 Z= 0.128 Angle : 0.647 11.376 18676 Z= 0.322 Chirality : 0.040 0.202 2092 Planarity : 0.004 0.059 2204 Dihedral : 23.019 157.656 3515 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.49 % Allowed : 24.79 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1584 helix: 1.17 (0.19), residues: 779 sheet: -1.61 (0.54), residues: 66 loop : 0.12 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 92 TYR 0.040 0.002 TYR A 342 PHE 0.030 0.001 PHE A 54 TRP 0.023 0.001 TRP A 120 HIS 0.007 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13691) covalent geometry : angle 0.64677 / 0.32 (18676) hydrogen bonds : bond 0.03665 / 2.45 ( 567) hydrogen bonds : angle 4.36295 / 3.24 ( 1625) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7757 (tt) cc_final: 0.7444 (tp) REVERT: B 38 ASN cc_start: 0.7508 (p0) cc_final: 0.7218 (p0) REVERT: B 169 ARG cc_start: 0.8029 (mtt180) cc_final: 0.6397 (mtm180) REVERT: B 311 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5854 (mm-30) REVERT: C 263 ASP cc_start: 0.6048 (t0) cc_final: 0.5698 (t0) REVERT: D 38 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6599 (p0) REVERT: E 253 LEU cc_start: 0.7964 (tt) cc_final: 0.7546 (tt) outliers start: 30 outliers final: 29 residues processed: 216 average time/residue: 0.0906 time to fit residues: 29.8216 Evaluate side-chains 222 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [0, 96, 52, 86, 31, 33, 27, 139, 65, 143, 137] chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 137 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 ASN E 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.227178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.182633 restraints weight = 48271.163| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.87 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13692 Z= 0.176 Angle : 0.674 10.977 18676 Z= 0.335 Chirality : 0.040 0.189 2092 Planarity : 0.004 0.042 2204 Dihedral : 23.029 158.903 3515 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 25.25 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.22), residues: 1584 helix: 1.03 (0.19), residues: 779 sheet: -1.60 (0.55), residues: 66 loop : 0.07 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 92 TYR 0.044 0.002 TYR A 342 PHE 0.028 0.002 PHE A 54 TRP 0.022 0.002 TRP A 120 HIS 0.006 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (13691) covalent geometry : angle 0.67432 / 0.33 (18676) hydrogen bonds : bond 0.03876 / 2.59 ( 567) hydrogen bonds : angle 4.45507 / 3.30 ( 1625) Misc. bond : bond 0.00062 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7826 (tt) cc_final: 0.7546 (tp) REVERT: B 38 ASN cc_start: 0.7487 (p0) cc_final: 0.7213 (p0) REVERT: B 169 ARG cc_start: 0.8149 (mtt180) cc_final: 0.6363 (mtm180) REVERT: B 311 GLU cc_start: 0.6106 (mm-30) cc_final: 0.5781 (mm-30) REVERT: C 197 TYR cc_start: 0.8359 (t80) cc_final: 0.8081 (t80) REVERT: C 263 ASP cc_start: 0.6316 (t0) cc_final: 0.5948 (t0) REVERT: D 38 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6617 (p0) outliers start: 30 outliers final: 28 residues processed: 214 average time/residue: 0.0940 time to fit residues: 30.6470 Evaluate side-chains 218 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [82, 121, 15, 87, 116, 137, 6, 14, 13, 119, 125] chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 59 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.4456 r_free = 0.4456 target = 0.228760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.184336 restraints weight = 52073.114| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.93 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13692 Z= 0.132 Angle : 0.651 10.415 18676 Z= 0.323 Chirality : 0.039 0.185 2092 Planarity : 0.004 0.043 2204 Dihedral : 22.892 159.643 3515 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 25.49 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1584 helix: 1.13 (0.19), residues: 779 sheet: -1.53 (0.55), residues: 66 loop : 0.08 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 92 TYR 0.039 0.002 TYR A 342 PHE 0.030 0.001 PHE A 54 TRP 0.023 0.001 TRP A 120 HIS 0.005 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13691) covalent geometry : angle 0.65110 / 0.32 (18676) hydrogen bonds : bond 0.03684 / 2.45 ( 567) hydrogen bonds : angle 4.35266 / 3.23 ( 1625) Misc. bond : bond 0.00052 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.87 seconds wall clock time: 41 minutes 56.81 seconds (2516.81 seconds total)