Starting phenix.real_space_refine on Sat Feb 7 09:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.map" model { file = "/net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vx6_65406/02_2026/9vx6_65406.cif" } resolution = 2.64 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= 0.001 sd= 0.022 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 182 5.49 5 S 96 5.16 5 C 19285 2.51 5 N 5513 2.21 5 O 6315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31391 Number of models: 1 Model: "" Number of chains: 18 Chain: "L" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "R" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 426 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "S" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3705 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 26, 'TRANS': 440} Chain breaks: 1 Chain: "T" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3252 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "F" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 426 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 426 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "Q" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "N" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "O" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3705 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 26, 'TRANS': 440} Chain breaks: 1 Chain: "P" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3120 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 371} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 426 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "W" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3705 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 26, 'TRANS': 440} Chain breaks: 1 Chain: "Y" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3252 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3713 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 26, 'TRANS': 441} Chain breaks: 1 Chain: "X" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3137 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 2 Time building chain proxies: 7.62, per 1000 atoms: 0.24 Number of scatterers: 31391 At special positions: 0 Unit cell: (167.7, 161.2, 161.2, 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 96 16.00 P 182 15.00 O 6315 8.00 N 5513 7.00 C 19285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6382 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 40 sheets defined 32.2% alpha, 20.8% beta 67 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 23 through 31 removed outlier: 3.928A pdb=" N SER S 29 " --> pdb=" O ARG S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 66 removed outlier: 3.922A pdb=" N GLU S 54 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 114 removed outlier: 3.699A pdb=" N ILE S 112 " --> pdb=" O LYS S 108 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY S 113 " --> pdb=" O LEU S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 139 removed outlier: 3.508A pdb=" N ASP S 138 " --> pdb=" O GLN S 134 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY S 139 " --> pdb=" O ALA S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 159 removed outlier: 4.177A pdb=" N ARG S 157 " --> pdb=" O LYS S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 190 Processing helix chain 'S' and resid 202 through 206 Processing helix chain 'S' and resid 225 through 243 removed outlier: 3.522A pdb=" N THR S 235 " --> pdb=" O TRP S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 328 removed outlier: 3.600A pdb=" N HIS S 326 " --> pdb=" O ALA S 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 346 through 358 removed outlier: 3.631A pdb=" N ALA S 357 " --> pdb=" O ALA S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 429 through 440 removed outlier: 3.505A pdb=" N LEU S 440 " --> pdb=" O GLU S 436 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 469 removed outlier: 4.035A pdb=" N VAL S 467 " --> pdb=" O LYS S 463 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 484 Processing helix chain 'T' and resid 6 through 26 removed outlier: 3.639A pdb=" N ILE T 10 " --> pdb=" O THR T 6 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU T 13 " --> pdb=" O GLN T 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG T 20 " --> pdb=" O GLU T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 91 removed outlier: 3.758A pdb=" N TYR T 88 " --> pdb=" O GLN T 84 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY T 91 " --> pdb=" O ALA T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 136 No H-bonds generated for 'chain 'T' and resid 134 through 136' Processing helix chain 'T' and resid 137 through 143 Processing helix chain 'T' and resid 189 through 194 Processing helix chain 'T' and resid 216 through 224 removed outlier: 6.501A pdb=" N ALA T 221 " --> pdb=" O ARG T 218 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N CYS T 222 " --> pdb=" O THR T 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER T 223 " --> pdb=" O SER T 220 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU T 224 " --> pdb=" O ALA T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 241 Processing helix chain 'T' and resid 247 through 262 Processing helix chain 'T' and resid 354 through 364 removed outlier: 3.606A pdb=" N LEU T 358 " --> pdb=" O PHE T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 367 through 382 Processing helix chain 'O' and resid 16 through 18 No H-bonds generated for 'chain 'O' and resid 16 through 18' Processing helix chain 'O' and resid 23 through 31 Processing helix chain 'O' and resid 49 through 65 removed outlier: 3.649A pdb=" N GLU O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU O 61 " --> pdb=" O ARG O 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 99 No H-bonds generated for 'chain 'O' and resid 97 through 99' Processing helix chain 'O' and resid 105 through 114 Processing helix chain 'O' and resid 121 through 139 Processing helix chain 'O' and resid 151 through 159 removed outlier: 4.005A pdb=" N ARG O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 190 Processing helix chain 'O' and resid 202 through 206 Processing helix chain 'O' and resid 225 through 243 removed outlier: 3.776A pdb=" N ASN O 232 " --> pdb=" O GLY O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 328 removed outlier: 3.529A pdb=" N HIS O 326 " --> pdb=" O ALA O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 358 removed outlier: 4.237A pdb=" N GLY O 349 " --> pdb=" O GLU O 345 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA O 357 " --> pdb=" O ALA O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 439 removed outlier: 3.582A pdb=" N GLU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) Processing helix chain 'O' and resid 455 through 469 removed outlier: 3.503A pdb=" N ALA O 461 " --> pdb=" O PRO O 457 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL O 467 " --> pdb=" O LYS O 463 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 Processing helix chain 'P' and resid 6 through 26 removed outlier: 3.760A pdb=" N GLY P 12 " --> pdb=" O ASN P 8 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 91 removed outlier: 4.047A pdb=" N GLY P 91 " --> pdb=" O ALA P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 136 No H-bonds generated for 'chain 'P' and resid 134 through 136' Processing helix chain 'P' and resid 137 through 143 Processing helix chain 'P' and resid 185 through 194 removed outlier: 3.691A pdb=" N ILE P 190 " --> pdb=" O PRO P 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA P 191 " --> pdb=" O ARG P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 216 through 225 removed outlier: 4.075A pdb=" N THR P 219 " --> pdb=" O ASP P 216 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER P 220 " --> pdb=" O PRO P 217 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA P 221 " --> pdb=" O ARG P 218 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N CYS P 222 " --> pdb=" O THR P 219 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER P 223 " --> pdb=" O SER P 220 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU P 224 " --> pdb=" O ALA P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 231 removed outlier: 3.507A pdb=" N GLN P 230 " --> pdb=" O ASP P 227 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL P 231 " --> pdb=" O ILE P 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 227 through 231' Processing helix chain 'P' and resid 247 through 263 removed outlier: 3.650A pdb=" N ARG P 260 " --> pdb=" O ARG P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 Processing helix chain 'P' and resid 367 through 383 removed outlier: 3.721A pdb=" N LEU P 371 " --> pdb=" O LYS P 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 416 through 420 removed outlier: 3.905A pdb=" N GLY P 419 " --> pdb=" O PRO P 416 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 18 No H-bonds generated for 'chain 'W' and resid 16 through 18' Processing helix chain 'W' and resid 23 through 31 removed outlier: 3.994A pdb=" N SER W 29 " --> pdb=" O ARG W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 66 removed outlier: 3.790A pdb=" N GLU W 54 " --> pdb=" O SER W 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER W 65 " --> pdb=" O GLU W 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY W 66 " --> pdb=" O THR W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 114 removed outlier: 3.636A pdb=" N ILE W 112 " --> pdb=" O LYS W 108 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 138 removed outlier: 3.513A pdb=" N GLU W 132 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 159 removed outlier: 4.174A pdb=" N ARG W 157 " --> pdb=" O LYS W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 190 removed outlier: 3.560A pdb=" N LYS W 189 " --> pdb=" O MET W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 206 Processing helix chain 'W' and resid 225 through 243 Processing helix chain 'W' and resid 308 through 328 removed outlier: 3.734A pdb=" N HIS W 326 " --> pdb=" O ALA W 322 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 358 removed outlier: 3.585A pdb=" N GLY W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU W 356 " --> pdb=" O ALA W 352 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA W 357 " --> pdb=" O ALA W 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 429 through 440 removed outlier: 3.501A pdb=" N GLU W 435 " --> pdb=" O ALA W 431 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 469 removed outlier: 3.554A pdb=" N ALA W 461 " --> pdb=" O PRO W 457 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL W 467 " --> pdb=" O LYS W 463 " (cutoff:3.500A) Processing helix chain 'W' and resid 480 through 484 Processing helix chain 'Y' and resid 6 through 26 removed outlier: 3.687A pdb=" N ILE Y 10 " --> pdb=" O THR Y 6 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 91 removed outlier: 3.799A pdb=" N TYR Y 88 " --> pdb=" O GLN Y 84 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY Y 91 " --> pdb=" O ALA Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 136 No H-bonds generated for 'chain 'Y' and resid 134 through 136' Processing helix chain 'Y' and resid 137 through 143 Processing helix chain 'Y' and resid 144 through 146 No H-bonds generated for 'chain 'Y' and resid 144 through 146' Processing helix chain 'Y' and resid 189 through 194 Processing helix chain 'Y' and resid 236 through 241 Processing helix chain 'Y' and resid 248 through 263 removed outlier: 3.609A pdb=" N THR Y 263 " --> pdb=" O LEU Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 364 removed outlier: 3.653A pdb=" N LEU Y 358 " --> pdb=" O PHE Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 367 through 382 removed outlier: 3.620A pdb=" N LEU Y 371 " --> pdb=" O LYS Y 367 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Y 372 " --> pdb=" O SER Y 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Y 375 " --> pdb=" O LEU Y 371 " (cutoff:3.500A) Processing helix chain 'Y' and resid 416 through 420 Processing helix chain 'U' and resid 16 through 18 No H-bonds generated for 'chain 'U' and resid 16 through 18' Processing helix chain 'U' and resid 23 through 31 Processing helix chain 'U' and resid 49 through 65 removed outlier: 3.553A pdb=" N GLU U 54 " --> pdb=" O SER U 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 99 No H-bonds generated for 'chain 'U' and resid 97 through 99' Processing helix chain 'U' and resid 105 through 114 removed outlier: 3.504A pdb=" N LYS U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 138 Processing helix chain 'U' and resid 151 through 159 removed outlier: 3.964A pdb=" N ARG U 157 " --> pdb=" O LYS U 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 181 through 190 Processing helix chain 'U' and resid 201 through 206 removed outlier: 4.016A pdb=" N ILE U 205 " --> pdb=" O TRP U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 243 removed outlier: 3.695A pdb=" N ASN U 232 " --> pdb=" O GLY U 228 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER U 236 " --> pdb=" O ASN U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 328 Processing helix chain 'U' and resid 343 through 358 removed outlier: 4.222A pdb=" N GLY U 349 " --> pdb=" O GLU U 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU U 356 " --> pdb=" O ALA U 352 " (cutoff:3.500A) Processing helix chain 'U' and resid 429 through 439 removed outlier: 3.526A pdb=" N GLU U 435 " --> pdb=" O ALA U 431 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU U 436 " --> pdb=" O GLN U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 469 removed outlier: 3.607A pdb=" N ALA U 461 " --> pdb=" O PRO U 457 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL U 467 " --> pdb=" O LYS U 463 " (cutoff:3.500A) Processing helix chain 'U' and resid 480 through 484 Processing helix chain 'X' and resid 6 through 26 removed outlier: 3.598A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY X 12 " --> pdb=" O ASN X 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR X 25 " --> pdb=" O GLY X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 89 Processing helix chain 'X' and resid 90 through 92 No H-bonds generated for 'chain 'X' and resid 90 through 92' Processing helix chain 'X' and resid 134 through 138 Processing helix chain 'X' and resid 185 through 196 removed outlier: 3.677A pdb=" N ILE X 190 " --> pdb=" O PRO X 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA X 191 " --> pdb=" O ARG X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 263 Processing helix chain 'X' and resid 354 through 364 removed outlier: 3.733A pdb=" N LEU X 358 " --> pdb=" O PHE X 354 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 383 removed outlier: 3.861A pdb=" N GLN X 374 " --> pdb=" O ALA X 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 420 removed outlier: 3.839A pdb=" N GLY X 419 " --> pdb=" O PRO X 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.790A pdb=" N THR S 387 " --> pdb=" O TYR S 398 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL S 334 " --> pdb=" O ASP S 363 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL S 365 " --> pdb=" O VAL S 334 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE S 336 " --> pdb=" O VAL S 365 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL S 367 " --> pdb=" O ILE S 336 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS S 338 " --> pdb=" O VAL S 367 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS S 259 " --> pdb=" O PHE S 335 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU S 337 " --> pdb=" O CYS S 259 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL S 261 " --> pdb=" O LEU S 337 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA S 258 " --> pdb=" O ASP S 283 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP S 283 " --> pdb=" O ALA S 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'S' and resid 93 through 103 removed outlier: 4.374A pdb=" N GLU S 97 " --> pdb=" O ILE S 44 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL S 46 " --> pdb=" O GLU S 97 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLY S 99 " --> pdb=" O VAL S 46 " (cutoff:3.500A) removed outlier: 11.199A pdb=" N GLY S 48 " --> pdb=" O GLY S 99 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N THR S 101 " --> pdb=" O GLY S 48 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N VAL S 145 " --> pdb=" O VAL S 41 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS S 43 " --> pdb=" O VAL S 145 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE S 147 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY S 45 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA S 149 " --> pdb=" O GLY S 45 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL S 47 " --> pdb=" O ALA S 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 375 through 377 Processing sheet with id=AA5, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.687A pdb=" N GLY T 42 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE T 57 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA T 44 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG T 55 " --> pdb=" O ALA T 44 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL T 46 " --> pdb=" O MET T 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 76 through 80 Processing sheet with id=AA7, first strand: chain 'T' and resid 287 through 291 removed outlier: 6.873A pdb=" N PHE T 289 " --> pdb=" O ASN T 301 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASN T 301 " --> pdb=" O PHE T 289 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR T 291 " --> pdb=" O ASP T 299 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP T 299 " --> pdb=" O TYR T 291 " (cutoff:3.500A) removed outlier: 26.506A pdb=" N THR T 298 " --> pdb=" O PRO T 325 " (cutoff:3.500A) removed outlier: 17.589A pdb=" N ALA T 300 " --> pdb=" O PHE T 323 " (cutoff:3.500A) removed outlier: 13.836A pdb=" N PHE T 323 " --> pdb=" O ALA T 300 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL T 302 " --> pdb=" O HIS T 321 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR T 339 " --> pdb=" O SER T 324 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP T 334 " --> pdb=" O LEU T 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 176 through 182 removed outlier: 6.747A pdb=" N GLN T 230 " --> pdb=" O SER T 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 267 through 269 Processing sheet with id=AB1, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.858A pdb=" N THR O 387 " --> pdb=" O TYR O 398 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS O 394 " --> pdb=" O LEU O 391 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N CYS O 259 " --> pdb=" O PHE O 335 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU O 337 " --> pdb=" O CYS O 259 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL O 261 " --> pdb=" O LEU O 337 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA O 258 " --> pdb=" O ASP O 283 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP O 283 " --> pdb=" O ALA O 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'O' and resid 93 through 95 removed outlier: 8.693A pdb=" N ALA O 102 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL O 46 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 93 through 95 removed outlier: 8.925A pdb=" N VAL O 145 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS O 43 " --> pdb=" O VAL O 145 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE O 147 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY O 45 " --> pdb=" O ILE O 147 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA O 149 " --> pdb=" O GLY O 45 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL O 47 " --> pdb=" O ALA O 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 375 through 376 Processing sheet with id=AB6, first strand: chain 'P' and resid 43 through 45 Processing sheet with id=AB7, first strand: chain 'P' and resid 76 through 80 Processing sheet with id=AB8, first strand: chain 'P' and resid 287 through 292 removed outlier: 6.864A pdb=" N PHE P 289 " --> pdb=" O ASN P 301 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN P 301 " --> pdb=" O PHE P 289 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR P 291 " --> pdb=" O ASP P 299 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP P 299 " --> pdb=" O TYR P 291 " (cutoff:3.500A) removed outlier: 23.321A pdb=" N THR P 298 " --> pdb=" O SER P 324 " (cutoff:3.500A) removed outlier: 20.088A pdb=" N SER P 324 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 13.733A pdb=" N ALA P 300 " --> pdb=" O ALA P 322 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N ALA P 322 " --> pdb=" O ALA P 300 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL P 302 " --> pdb=" O HIS P 320 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N HIS P 320 " --> pdb=" O VAL P 302 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER P 304 " --> pdb=" O VAL P 318 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL P 318 " --> pdb=" O SER P 304 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE P 306 " --> pdb=" O SER P 316 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP P 334 " --> pdb=" O LEU P 171 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET P 402 " --> pdb=" O THR P 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 211 through 213 removed outlier: 3.777A pdb=" N SER P 213 " --> pdb=" O TYR P 178 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR P 178 " --> pdb=" O SER P 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'W' and resid 5 through 7 removed outlier: 3.856A pdb=" N THR W 387 " --> pdb=" O TYR W 398 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS W 394 " --> pdb=" O LEU W 391 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL W 334 " --> pdb=" O ASP W 363 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL W 365 " --> pdb=" O VAL W 334 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE W 336 " --> pdb=" O VAL W 365 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL W 367 " --> pdb=" O ILE W 336 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS W 338 " --> pdb=" O VAL W 367 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA W 258 " --> pdb=" O ASP W 283 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP W 283 " --> pdb=" O ALA W 258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'W' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'W' and resid 93 through 103 removed outlier: 4.105A pdb=" N GLU W 97 " --> pdb=" O ILE W 44 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL W 46 " --> pdb=" O GLU W 97 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N GLY W 99 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N GLY W 48 " --> pdb=" O GLY W 99 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N THR W 101 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL W 145 " --> pdb=" O VAL W 41 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS W 43 " --> pdb=" O VAL W 145 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE W 147 " --> pdb=" O LYS W 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY W 45 " --> pdb=" O ILE W 147 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA W 149 " --> pdb=" O GLY W 45 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL W 47 " --> pdb=" O ALA W 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 375 through 377 Processing sheet with id=AC6, first strand: chain 'Y' and resid 29 through 32 removed outlier: 6.605A pdb=" N GLY Y 42 " --> pdb=" O ILE Y 57 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE Y 57 " --> pdb=" O GLY Y 42 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA Y 44 " --> pdb=" O ARG Y 55 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG Y 55 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL Y 46 " --> pdb=" O MET Y 53 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 76 through 80 Processing sheet with id=AC8, first strand: chain 'Y' and resid 327 through 329 removed outlier: 4.701A pdb=" N TRP Y 334 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 176 through 177 Processing sheet with id=AD1, first strand: chain 'Y' and resid 180 through 182 removed outlier: 5.247A pdb=" N SER Y 181 " --> pdb=" O ASP Y 227 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 267 through 270 removed outlier: 3.557A pdb=" N ALA Y 275 " --> pdb=" O ASP Y 270 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS Y 321 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 267 through 270 removed outlier: 3.557A pdb=" N ALA Y 275 " --> pdb=" O ASP Y 270 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS Y 321 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR Y 339 " --> pdb=" O SER Y 324 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 5 through 7 removed outlier: 3.798A pdb=" N THR U 387 " --> pdb=" O TYR U 398 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS U 394 " --> pdb=" O LEU U 391 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS U 259 " --> pdb=" O PHE U 335 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU U 337 " --> pdb=" O CYS U 259 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL U 261 " --> pdb=" O LEU U 337 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA U 258 " --> pdb=" O ASP U 283 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP U 283 " --> pdb=" O ALA U 258 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AD6, first strand: chain 'U' and resid 93 through 95 removed outlier: 8.711A pdb=" N ALA U 102 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL U 46 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 93 through 95 removed outlier: 8.959A pdb=" N VAL U 145 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS U 43 " --> pdb=" O VAL U 145 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE U 147 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY U 45 " --> pdb=" O ILE U 147 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA U 149 " --> pdb=" O GLY U 45 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL U 47 " --> pdb=" O ALA U 149 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 375 through 376 Processing sheet with id=AD9, first strand: chain 'X' and resid 29 through 32 removed outlier: 5.193A pdb=" N ARG X 55 " --> pdb=" O VAL X 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 76 through 80 Processing sheet with id=AE2, first strand: chain 'X' and resid 287 through 292 removed outlier: 6.173A pdb=" N ARG X 287 " --> pdb=" O VAL X 302 " (cutoff:3.500A) removed outlier: 26.240A pdb=" N THR X 298 " --> pdb=" O PRO X 325 " (cutoff:3.500A) removed outlier: 17.511A pdb=" N ALA X 300 " --> pdb=" O PHE X 323 " (cutoff:3.500A) removed outlier: 13.668A pdb=" N PHE X 323 " --> pdb=" O ALA X 300 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL X 302 " --> pdb=" O HIS X 321 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TRP X 334 " --> pdb=" O LEU X 171 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 210 through 211 Processing sheet with id=AE4, first strand: chain 'X' and resid 267 through 270 removed outlier: 3.562A pdb=" N ALA X 275 " --> pdb=" O ASP X 270 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2955 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5123 1.32 - 1.44: 9724 1.44 - 1.57: 17110 1.57 - 1.69: 354 1.69 - 1.82: 176 Bond restraints: 32487 Sorted by residual: bond pdb=" C THR W 329 " pdb=" N LEU W 330 " ideal model delta sigma weight residual 1.331 1.191 0.140 2.83e-02 1.25e+03 2.43e+01 bond pdb=" C THR S 329 " pdb=" N LEU S 330 " ideal model delta sigma weight residual 1.331 1.205 0.126 2.83e-02 1.25e+03 1.97e+01 bond pdb=" C ILE Y 225 " pdb=" N VAL Y 226 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.46e-02 4.69e+03 1.18e+01 bond pdb=" C SER U 141 " pdb=" N ARG U 142 " ideal model delta sigma weight residual 1.328 1.271 0.056 1.67e-02 3.59e+03 1.13e+01 bond pdb=" C TYR Y 184 " pdb=" N GLU Y 185 " ideal model delta sigma weight residual 1.331 1.237 0.094 2.83e-02 1.25e+03 1.11e+01 ... (remaining 32482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 44409 3.93 - 7.87: 345 7.87 - 11.80: 10 11.80 - 15.74: 3 15.74 - 19.67: 2 Bond angle restraints: 44769 Sorted by residual: angle pdb=" C ARG S 303 " pdb=" N HIS S 304 " pdb=" CA HIS S 304 " ideal model delta sigma weight residual 121.61 141.28 -19.67 1.39e+00 5.18e-01 2.00e+02 angle pdb=" C ARG W 303 " pdb=" N HIS W 304 " pdb=" CA HIS W 304 " ideal model delta sigma weight residual 121.27 139.19 -17.92 3.40e+00 8.65e-02 2.78e+01 angle pdb=" C ASP P 203 " pdb=" N TRP P 204 " pdb=" CA TRP P 204 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C TYR Y 184 " pdb=" N GLU Y 185 " pdb=" CA GLU Y 185 " ideal model delta sigma weight residual 120.97 134.99 -14.02 2.84e+00 1.24e-01 2.44e+01 angle pdb=" C3' DA Q 19 " pdb=" O3' DA Q 19 " pdb=" P DT Q 20 " ideal model delta sigma weight residual 120.20 127.05 -6.85 1.50e+00 4.44e-01 2.09e+01 ... (remaining 44764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 18535 34.92 - 69.85: 623 69.85 - 104.77: 58 104.77 - 139.69: 4 139.69 - 174.61: 9 Dihedral angle restraints: 19229 sinusoidal: 9273 harmonic: 9956 Sorted by residual: dihedral pdb=" CA MET P 47 " pdb=" C MET P 47 " pdb=" N ASN P 48 " pdb=" CA ASN P 48 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ILE X 206 " pdb=" C ILE X 206 " pdb=" N ASN X 207 " pdb=" CA ASN X 207 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS U 118 " pdb=" C HIS U 118 " pdb=" N TYR U 119 " pdb=" CA TYR U 119 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 19226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 4693 0.121 - 0.242: 214 0.242 - 0.363: 3 0.363 - 0.484: 0 0.484 - 0.605: 1 Chirality restraints: 4911 Sorted by residual: chirality pdb=" P DT M 16 " pdb=" OP1 DT M 16 " pdb=" OP2 DT M 16 " pdb=" O5' DT M 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" CA ILE W 245 " pdb=" N ILE W 245 " pdb=" C ILE W 245 " pdb=" CB ILE W 245 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE X 43 " pdb=" CA ILE X 43 " pdb=" CG1 ILE X 43 " pdb=" CG2 ILE X 43 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4908 not shown) Planarity restraints: 5144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP O 445 " 0.030 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP O 445 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP O 445 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP O 445 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP O 445 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP O 445 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP O 445 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 445 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 445 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP O 445 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 231 " -0.028 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP W 231 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP W 231 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP W 231 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP W 231 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP W 231 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP W 231 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 231 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 231 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP W 231 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 445 " -0.018 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP W 445 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP W 445 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP W 445 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP W 445 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP W 445 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP W 445 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 445 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 445 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP W 445 " -0.000 2.00e-02 2.50e+03 ... (remaining 5141 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5830 2.76 - 3.29: 26440 3.29 - 3.83: 54215 3.83 - 4.36: 66876 4.36 - 4.90: 108945 Nonbonded interactions: 262306 Sorted by model distance: nonbonded pdb=" OG SER S 257 " pdb=" OH TYR S 323 " model vdw 2.223 3.040 nonbonded pdb=" OG SER X 181 " pdb=" OE1 GLN X 230 " model vdw 2.249 3.040 nonbonded pdb=" OP2 DG L 9 " pdb=" NH2 ARG T 326 " model vdw 2.251 3.120 nonbonded pdb=" O PRO P 217 " pdb=" OG SER P 223 " model vdw 2.254 3.040 nonbonded pdb=" OG SER W 257 " pdb=" OH TYR W 323 " model vdw 2.263 3.040 ... (remaining 262301 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 'E' selection = chain 'I' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'S' selection = (chain 'U' and resid 1 through 484) selection = chain 'W' } ncs_group { reference = (chain 'P' and (resid 4 through 294 or (resid 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 through 420)) selection = (chain 'T' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 145 or resid 161 through 206 or (resid 207 and (name N or n \ ame CA or name C or name O or name CB )) or resid 208 through 313 or (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 42 \ 0)) selection = (chain 'X' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 160 or resid 162 through 206 or (resid 207 and (name N or n \ ame CA or name C or name O or name CB )) or resid 208 through 294 or (resid 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 31 \ 3 or (resid 314 and (name N or name CA or name C or name O or name CB )) or resi \ d 315 through 420)) selection = (chain 'Y' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 145 or resid 161 through 206 or (resid 207 and (name N or n \ ame CA or name C or name O or name CB )) or resid 208 through 313 or (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 42 \ 0)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 40.890 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: 0.050 Extract box with map and model: 0.890 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.560 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 0.140 32487 Z= 0.524 Angle : 1.023 19.672 44769 Z= 0.557 Chirality : 0.060 0.605 4911 Planarity : 0.007 0.059 5144 Dihedral : 15.690 174.614 12847 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.11), residues: 3416 helix: -4.12 (0.08), residues: 967 sheet: -1.06 (0.18), residues: 814 loop : -2.69 (0.12), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG U 157 TYR 0.028 0.004 TYR U 413 PHE 0.036 0.004 PHE X 133 TRP 0.059 0.005 TRP O 445 HIS 0.021 0.003 HIS X 321 Details of bonding type rmsd covalent geometry : bond 0.01223 (32487) covalent geometry : angle 1.02288 (44769) hydrogen bonds : bond 0.27351 ( 1196) hydrogen bonds : angle 9.67206 ( 3291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7288 (mp0) REVERT: S 108 LYS cc_start: 0.7681 (mttt) cc_final: 0.7469 (mppt) REVERT: S 249 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8131 (ttt90) REVERT: S 310 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7284 (mm-30) REVERT: T 287 ARG cc_start: 0.5447 (ttm170) cc_final: 0.4872 (ttt-90) REVERT: T 347 ASN cc_start: 0.7673 (p0) cc_final: 0.7229 (m110) REVERT: O 41 VAL cc_start: 0.9034 (t) cc_final: 0.8708 (t) REVERT: O 111 LYS cc_start: 0.8324 (pttp) cc_final: 0.8094 (ptpt) REVERT: O 114 LYS cc_start: 0.8186 (mptt) cc_final: 0.7976 (mtpt) REVERT: O 314 LYS cc_start: 0.7871 (tppt) cc_final: 0.7394 (tptm) REVERT: O 444 ASN cc_start: 0.7963 (t0) cc_final: 0.7464 (m110) REVERT: P 6 THR cc_start: 0.7960 (p) cc_final: 0.7740 (t) REVERT: P 55 ARG cc_start: 0.6843 (mmm160) cc_final: 0.6179 (mtm110) REVERT: P 60 GLN cc_start: 0.8296 (tp40) cc_final: 0.7962 (tp40) REVERT: P 178 TYR cc_start: 0.6249 (m-80) cc_final: 0.5989 (m-80) REVERT: P 306 PHE cc_start: 0.6211 (m-10) cc_final: 0.5983 (m-80) REVERT: P 307 LYS cc_start: 0.7532 (ptpp) cc_final: 0.7016 (mmtm) REVERT: W 61 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6358 (pt0) REVERT: W 295 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7523 (mmm160) REVERT: W 314 LYS cc_start: 0.8218 (tppt) cc_final: 0.7869 (tmtt) REVERT: Y 13 GLU cc_start: 0.7199 (tp30) cc_final: 0.6956 (tp30) REVERT: Y 216 ASP cc_start: 0.6407 (t0) cc_final: 0.5909 (m-30) REVERT: Y 247 GLU cc_start: 0.6680 (mt-10) cc_final: 0.5974 (tp30) REVERT: Y 301 ASN cc_start: 0.7000 (t0) cc_final: 0.6736 (t0) REVERT: U 108 LYS cc_start: 0.7784 (mttt) cc_final: 0.7494 (mmmt) REVERT: U 111 LYS cc_start: 0.8234 (pttp) cc_final: 0.8014 (pttm) REVERT: U 128 GLU cc_start: 0.7573 (tp30) cc_final: 0.7173 (tp30) REVERT: U 226 ILE cc_start: 0.7906 (mp) cc_final: 0.7681 (tp) REVERT: U 252 LEU cc_start: 0.8556 (mt) cc_final: 0.8240 (mt) REVERT: U 314 LYS cc_start: 0.8153 (tppt) cc_final: 0.7906 (tptp) REVERT: U 482 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7558 (mtm-85) REVERT: X 9 GLN cc_start: 0.7402 (mt0) cc_final: 0.6668 (tt0) REVERT: X 165 LEU cc_start: 0.7870 (mt) cc_final: 0.7523 (pp) REVERT: X 365 LEU cc_start: 0.8051 (mm) cc_final: 0.7850 (mp) REVERT: X 412 ASP cc_start: 0.7486 (p0) cc_final: 0.7267 (m-30) outliers start: 0 outliers final: 2 residues processed: 535 average time/residue: 0.9124 time to fit residues: 553.6199 Evaluate side-chains 256 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain W residue 138 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 74 HIS S 160 ASN S 181 ASN S 304 HIS ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 444 ASN T 60 GLN T 84 GLN T 93 ASN T 215 HIS T 235 ASN T 262 GLN T 273 HIS O 74 HIS O 86 ASN O 160 ASN O 272 GLN O 304 HIS ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 HIS P 8 ASN ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 ASN P 301 ASN P 321 HIS P 352 HIS W 22 GLN W 74 HIS W 160 ASN W 213 GLN W 224 GLN W 304 HIS ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Y 84 GLN Y 262 GLN Y 273 HIS Y 288 ASN Y 352 HIS U 160 ASN U 272 GLN U 304 HIS ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 ASN X 253 HIS X 257 GLN X 320 HIS X 321 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103671 restraints weight = 48885.599| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.98 r_work: 0.3298 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32487 Z= 0.141 Angle : 0.624 17.843 44769 Z= 0.332 Chirality : 0.041 0.172 4911 Planarity : 0.005 0.069 5144 Dihedral : 19.162 177.773 6137 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.29 % Allowed : 9.80 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.13), residues: 3416 helix: -1.60 (0.14), residues: 1023 sheet: -0.71 (0.18), residues: 823 loop : -2.08 (0.13), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 201 TYR 0.027 0.001 TYR X 261 PHE 0.051 0.002 PHE Y 354 TRP 0.019 0.001 TRP O 445 HIS 0.013 0.001 HIS O 392 Details of bonding type rmsd covalent geometry : bond 0.00306 (32487) covalent geometry : angle 0.62389 (44769) hydrogen bonds : bond 0.05066 ( 1196) hydrogen bonds : angle 5.49542 ( 3291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 327 time to evaluate : 1.174 Fit side-chains REVERT: S 4 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7788 (mp0) REVERT: S 95 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: S 123 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7145 (tm-30) REVERT: S 249 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8615 (ttp80) REVERT: S 310 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7201 (mm-30) REVERT: T 188 LYS cc_start: 0.5924 (mmtt) cc_final: 0.5630 (mtpm) REVERT: T 235 ASN cc_start: 0.6745 (t0) cc_final: 0.6055 (p0) REVERT: T 237 LYS cc_start: 0.7711 (mttp) cc_final: 0.7411 (mptp) REVERT: T 238 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6919 (mm-30) REVERT: T 297 LYS cc_start: 0.6448 (mmtm) cc_final: 0.6246 (tptm) REVERT: T 347 ASN cc_start: 0.7492 (p0) cc_final: 0.7174 (m110) REVERT: O 38 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8276 (tt) REVERT: O 111 LYS cc_start: 0.8514 (pttp) cc_final: 0.8292 (ptpt) REVERT: O 314 LYS cc_start: 0.8148 (tppt) cc_final: 0.7818 (tptm) REVERT: O 444 ASN cc_start: 0.8215 (t0) cc_final: 0.7835 (m110) REVERT: O 477 ILE cc_start: 0.8240 (mt) cc_final: 0.8029 (mm) REVERT: P 16 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: P 230 GLN cc_start: 0.5409 (tp-100) cc_final: 0.4937 (mt0) REVERT: P 261 TYR cc_start: 0.6946 (t80) cc_final: 0.6448 (t80) REVERT: P 307 LYS cc_start: 0.7708 (ptpp) cc_final: 0.7287 (mmtm) REVERT: Y 4 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7498 (ttmm) REVERT: Y 224 GLU cc_start: 0.7335 (pt0) cc_final: 0.6683 (pp20) REVERT: Y 245 ILE cc_start: 0.8281 (mm) cc_final: 0.8002 (tp) REVERT: Y 247 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6008 (tp30) REVERT: U 61 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8041 (mm-30) REVERT: U 120 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7391 (tpm170) REVERT: U 226 ILE cc_start: 0.7860 (mp) cc_final: 0.7576 (tp) REVERT: U 314 LYS cc_start: 0.8395 (tppt) cc_final: 0.8181 (tptm) REVERT: X 9 GLN cc_start: 0.7221 (mt0) cc_final: 0.6873 (tt0) REVERT: X 207 ASN cc_start: 0.7423 (m-40) cc_final: 0.7102 (m110) REVERT: X 231 VAL cc_start: 0.6865 (t) cc_final: 0.6507 (m) REVERT: X 414 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7588 (ttt90) outliers start: 67 outliers final: 16 residues processed: 373 average time/residue: 0.7274 time to fit residues: 316.1589 Evaluate side-chains 252 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 MET Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain T residue 252 SER Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 376 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain U residue 120 ARG Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain X residue 222 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 223 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 317 optimal weight: 0.5980 chunk 346 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 304 HIS ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN T 257 GLN O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 HIS O 416 ASN O 446 ASN P 106 HIS ** P 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN W 224 GLN W 304 HIS ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 416 ASN Y 195 ASN ** U 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 HIS ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100973 restraints weight = 48551.368| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.15 r_work: 0.3239 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32487 Z= 0.183 Angle : 0.609 15.422 44769 Z= 0.323 Chirality : 0.043 0.148 4911 Planarity : 0.005 0.070 5144 Dihedral : 18.950 175.695 6133 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.76 % Allowed : 11.98 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3416 helix: -0.23 (0.16), residues: 1012 sheet: -0.54 (0.18), residues: 822 loop : -1.83 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 93 TYR 0.021 0.002 TYR P 291 PHE 0.048 0.002 PHE T 354 TRP 0.024 0.002 TRP X 204 HIS 0.009 0.001 HIS O 392 Details of bonding type rmsd covalent geometry : bond 0.00424 (32487) covalent geometry : angle 0.60923 (44769) hydrogen bonds : bond 0.04754 ( 1196) hydrogen bonds : angle 5.08812 ( 3291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7698 (mp0) REVERT: S 123 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7331 (mm-30) REVERT: S 310 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7211 (mm-30) REVERT: S 450 MET cc_start: 0.9173 (mtm) cc_final: 0.8898 (mtp) REVERT: T 188 LYS cc_start: 0.5965 (mmtt) cc_final: 0.5607 (mtpm) REVERT: T 202 PHE cc_start: 0.6485 (m-80) cc_final: 0.6228 (m-80) REVERT: T 235 ASN cc_start: 0.6539 (t0) cc_final: 0.6080 (p0) REVERT: T 237 LYS cc_start: 0.7691 (mttp) cc_final: 0.7401 (mptp) REVERT: T 333 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7526 (tm-30) REVERT: T 347 ASN cc_start: 0.7530 (p0) cc_final: 0.7187 (m110) REVERT: T 354 PHE cc_start: 0.6235 (t80) cc_final: 0.5989 (t80) REVERT: O 38 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8162 (tt) REVERT: O 314 LYS cc_start: 0.8144 (tppt) cc_final: 0.7812 (tptm) REVERT: P 16 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: P 33 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7967 (tpt-90) REVERT: P 43 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7804 (pt) REVERT: P 47 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6592 (ttp) REVERT: P 55 ARG cc_start: 0.7354 (mmm160) cc_final: 0.6500 (mtm110) REVERT: P 68 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7823 (tppt) REVERT: P 261 TYR cc_start: 0.7094 (t80) cc_final: 0.6544 (t80) REVERT: P 307 LYS cc_start: 0.7801 (ptpp) cc_final: 0.7357 (mmtm) REVERT: W 38 LEU cc_start: 0.7857 (mm) cc_final: 0.7559 (mt) REVERT: W 360 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: Y 4 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7794 (ttmm) REVERT: Y 200 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6682 (ttmt) REVERT: Y 224 GLU cc_start: 0.7484 (pt0) cc_final: 0.6742 (pp20) REVERT: Y 247 GLU cc_start: 0.6605 (mt-10) cc_final: 0.5778 (mm-30) REVERT: Y 312 GLU cc_start: 0.6604 (mp0) cc_final: 0.6387 (mp0) REVERT: U 61 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8001 (mm-30) REVERT: U 95 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: U 114 LYS cc_start: 0.8664 (mptt) cc_final: 0.8438 (mtmt) REVERT: U 120 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7374 (tpm170) REVERT: U 226 ILE cc_start: 0.7924 (mp) cc_final: 0.7552 (tp) REVERT: X 9 GLN cc_start: 0.7233 (mt0) cc_final: 0.6800 (tt0) REVERT: X 16 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: X 114 SER cc_start: 0.8003 (t) cc_final: 0.7796 (m) REVERT: X 231 VAL cc_start: 0.6917 (t) cc_final: 0.6612 (m) REVERT: X 272 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (m-30) outliers start: 81 outliers final: 30 residues processed: 307 average time/residue: 0.6848 time to fit residues: 245.3731 Evaluate side-chains 269 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 360 GLU Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 200 LYS Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain Y residue 412 ASP Chi-restraints excluded: chain U residue 40 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain U residue 120 ARG Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 222 CYS Chi-restraints excluded: chain X residue 272 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 133 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 156 optimal weight: 2.9990 chunk 309 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 352 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 74 HIS ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 444 ASN ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 HIS ** P 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 ASN X 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103201 restraints weight = 48384.815| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.97 r_work: 0.3281 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32487 Z= 0.121 Angle : 0.539 13.286 44769 Z= 0.287 Chirality : 0.040 0.168 4911 Planarity : 0.004 0.067 5144 Dihedral : 18.803 176.869 6133 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.76 % Allowed : 12.59 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3416 helix: 0.38 (0.16), residues: 1030 sheet: -0.25 (0.18), residues: 820 loop : -1.64 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 93 TYR 0.021 0.001 TYR P 291 PHE 0.034 0.001 PHE T 354 TRP 0.026 0.001 TRP P 204 HIS 0.005 0.001 HIS X 215 Details of bonding type rmsd covalent geometry : bond 0.00267 (32487) covalent geometry : angle 0.53888 (44769) hydrogen bonds : bond 0.03838 ( 1196) hydrogen bonds : angle 4.76695 ( 3291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7751 (mp0) REVERT: S 123 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7435 (tm-30) REVERT: S 310 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7188 (mm-30) REVERT: S 392 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8000 (m90) REVERT: S 450 MET cc_start: 0.9192 (mtm) cc_final: 0.8854 (mtp) REVERT: T 51 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7331 (tp40) REVERT: T 165 LEU cc_start: 0.8604 (mt) cc_final: 0.8195 (pp) REVERT: T 188 LYS cc_start: 0.5976 (mmtt) cc_final: 0.5662 (mtpm) REVERT: T 235 ASN cc_start: 0.6594 (t0) cc_final: 0.6078 (p0) REVERT: T 237 LYS cc_start: 0.7635 (mttp) cc_final: 0.7420 (mptp) REVERT: T 333 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7489 (tm-30) REVERT: O 314 LYS cc_start: 0.8218 (tppt) cc_final: 0.7834 (tptm) REVERT: P 47 MET cc_start: 0.6812 (ttp) cc_final: 0.6461 (ttt) REVERT: P 55 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6465 (mtm110) REVERT: P 68 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7781 (tppt) REVERT: P 205 VAL cc_start: 0.5757 (OUTLIER) cc_final: 0.5271 (t) REVERT: P 242 HIS cc_start: 0.7268 (t-90) cc_final: 0.7062 (p90) REVERT: P 261 TYR cc_start: 0.7136 (t80) cc_final: 0.6642 (t80) REVERT: P 307 LYS cc_start: 0.7928 (ptpp) cc_final: 0.7463 (mmtm) REVERT: W 142 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6704 (ttm110) REVERT: W 250 MET cc_start: 0.8550 (ttt) cc_final: 0.8349 (ttt) REVERT: W 299 GLU cc_start: 0.7445 (pm20) cc_final: 0.7208 (pm20) REVERT: W 360 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: W 466 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8140 (pt0) REVERT: Y 4 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8332 (tptt) REVERT: Y 224 GLU cc_start: 0.7344 (pt0) cc_final: 0.6704 (pp20) REVERT: Y 247 GLU cc_start: 0.6504 (mt-10) cc_final: 0.5766 (mm-30) REVERT: Y 312 GLU cc_start: 0.6728 (mp0) cc_final: 0.6445 (mp0) REVERT: U 95 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: U 114 LYS cc_start: 0.8714 (mptt) cc_final: 0.8498 (mtmt) REVERT: U 226 ILE cc_start: 0.7921 (mp) cc_final: 0.7657 (tp) REVERT: X 9 GLN cc_start: 0.7228 (mt0) cc_final: 0.6821 (tt0) REVERT: X 16 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: X 168 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: X 207 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7085 (m110) REVERT: X 231 VAL cc_start: 0.6956 (t) cc_final: 0.6682 (m) outliers start: 81 outliers final: 26 residues processed: 313 average time/residue: 0.7435 time to fit residues: 270.9731 Evaluate side-chains 263 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 253 GLU Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 328 GLU Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 191 MET Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 360 GLU Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain U residue 40 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 168 MET Chi-restraints excluded: chain X residue 175 ASN Chi-restraints excluded: chain X residue 207 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 233 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 236 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 444 ASN ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 444 ASN ** P 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 GLN ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 352 HIS X 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099832 restraints weight = 48767.339| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.92 r_work: 0.3231 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32487 Z= 0.187 Angle : 0.590 12.881 44769 Z= 0.314 Chirality : 0.043 0.190 4911 Planarity : 0.004 0.061 5144 Dihedral : 18.801 172.117 6133 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.76 % Allowed : 13.48 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3416 helix: 0.49 (0.16), residues: 1043 sheet: -0.23 (0.18), residues: 789 loop : -1.56 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 93 TYR 0.023 0.002 TYR X 261 PHE 0.039 0.002 PHE T 354 TRP 0.017 0.001 TRP P 204 HIS 0.015 0.001 HIS Y 352 Details of bonding type rmsd covalent geometry : bond 0.00437 (32487) covalent geometry : angle 0.58955 (44769) hydrogen bonds : bond 0.04250 ( 1196) hydrogen bonds : angle 4.82496 ( 3291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 238 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 310 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7304 (mm-30) REVERT: S 450 MET cc_start: 0.9190 (mtm) cc_final: 0.8907 (mtp) REVERT: T 51 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7205 (tp40) REVERT: T 171 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6577 (mp) REVERT: T 188 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5598 (mtpm) REVERT: T 235 ASN cc_start: 0.6672 (t0) cc_final: 0.6153 (p0) REVERT: T 237 LYS cc_start: 0.7646 (mttp) cc_final: 0.7438 (mptp) REVERT: T 333 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7541 (tm-30) REVERT: O 314 LYS cc_start: 0.8125 (tppt) cc_final: 0.7751 (tptm) REVERT: P 16 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: P 43 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7812 (pt) REVERT: P 47 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6567 (ttt) REVERT: P 261 TYR cc_start: 0.7199 (t80) cc_final: 0.6635 (t80) REVERT: P 307 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7577 (mmtm) REVERT: P 402 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6814 (mmm) REVERT: W 87 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (mp-120) REVERT: W 299 GLU cc_start: 0.7668 (pm20) cc_final: 0.7418 (pm20) REVERT: Y 224 GLU cc_start: 0.7373 (pt0) cc_final: 0.6809 (pp20) REVERT: Y 247 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5731 (mm-30) REVERT: Y 312 GLU cc_start: 0.6719 (mp0) cc_final: 0.6491 (mp0) REVERT: U 95 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: U 114 LYS cc_start: 0.8712 (mptt) cc_final: 0.8441 (mtmt) REVERT: U 226 ILE cc_start: 0.7868 (mp) cc_final: 0.7553 (tp) REVERT: U 268 GLU cc_start: 0.8351 (tt0) cc_final: 0.8138 (pt0) REVERT: X 9 GLN cc_start: 0.7156 (mt0) cc_final: 0.6700 (tt0) REVERT: X 207 ASN cc_start: 0.7445 (m110) cc_final: 0.7197 (m110) REVERT: X 231 VAL cc_start: 0.6966 (t) cc_final: 0.6727 (m) outliers start: 81 outliers final: 39 residues processed: 285 average time/residue: 0.7261 time to fit residues: 242.1077 Evaluate side-chains 264 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 376 LEU Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain S residue 444 ASN Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 171 LEU Chi-restraints excluded: chain T residue 252 SER Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 328 GLU Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 402 MET Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 191 MET Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 257 GLN Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 87 GLN Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain Y residue 412 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 40 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain X residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 341 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 297 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 215 HIS O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 ASN ** W 326 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 = 0.3786 r_free = 0.3786 target = 0.133392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102995 restraints weight = 48414.401| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.10 r_work: 0.3256 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32487 Z= 0.127 Angle : 0.536 12.248 44769 Z= 0.286 Chirality : 0.040 0.171 4911 Planarity : 0.004 0.062 5144 Dihedral : 18.666 172.787 6133 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.46 % Allowed : 14.33 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3416 helix: 0.76 (0.17), residues: 1044 sheet: -0.02 (0.19), residues: 792 loop : -1.46 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 93 TYR 0.020 0.001 TYR P 291 PHE 0.030 0.001 PHE T 354 TRP 0.020 0.001 TRP P 204 HIS 0.007 0.001 HIS X 215 Details of bonding type rmsd covalent geometry : bond 0.00284 (32487) covalent geometry : angle 0.53648 (44769) hydrogen bonds : bond 0.03703 ( 1196) hydrogen bonds : angle 4.62519 ( 3291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 310 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7248 (mm-30) REVERT: S 392 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7965 (m90) REVERT: T 51 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7167 (tp40) REVERT: T 56 MET cc_start: 0.8681 (mmt) cc_final: 0.8044 (mmt) REVERT: T 171 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6577 (mp) REVERT: T 188 LYS cc_start: 0.5945 (mmtt) cc_final: 0.5564 (mtpm) REVERT: T 235 ASN cc_start: 0.6709 (t0) cc_final: 0.6149 (p0) REVERT: T 237 LYS cc_start: 0.7609 (mttp) cc_final: 0.7404 (mptp) REVERT: T 333 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7457 (tm-30) REVERT: O 314 LYS cc_start: 0.8128 (tppt) cc_final: 0.7767 (tptm) REVERT: P 16 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: P 47 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6468 (ttt) REVERT: P 55 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6373 (mtm110) REVERT: P 68 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7849 (tppt) REVERT: P 261 TYR cc_start: 0.7140 (t80) cc_final: 0.6638 (t80) REVERT: P 307 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7663 (mmtm) REVERT: W 87 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8048 (mp-120) REVERT: W 142 ARG cc_start: 0.6979 (ttm170) cc_final: 0.6606 (ttm110) REVERT: Y 224 GLU cc_start: 0.7361 (pt0) cc_final: 0.6753 (pm20) REVERT: Y 312 GLU cc_start: 0.6707 (mp0) cc_final: 0.6356 (mp0) REVERT: U 95 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: U 114 LYS cc_start: 0.8678 (mptt) cc_final: 0.8367 (mtmt) REVERT: U 226 ILE cc_start: 0.7819 (mp) cc_final: 0.7508 (tp) REVERT: U 268 GLU cc_start: 0.8315 (tt0) cc_final: 0.8100 (pt0) REVERT: U 449 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: X 9 GLN cc_start: 0.7153 (mt0) cc_final: 0.6711 (tt0) REVERT: X 171 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8007 (mp) REVERT: X 207 ASN cc_start: 0.7571 (m110) cc_final: 0.7279 (m110) REVERT: X 231 VAL cc_start: 0.6945 (t) cc_final: 0.6716 (m) outliers start: 72 outliers final: 32 residues processed: 283 average time/residue: 0.7396 time to fit residues: 244.8132 Evaluate side-chains 262 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 376 LEU Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 171 LEU Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 377 MET Chi-restraints excluded: chain T residue 402 MET Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 257 GLN Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 87 GLN Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 40 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 449 GLN Chi-restraints excluded: chain U residue 485 ILE Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 168 optimal weight: 0.0020 chunk 296 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 253 HIS ** W 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102201 restraints weight = 48651.776| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.07 r_work: 0.3239 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32487 Z= 0.142 Angle : 0.545 11.988 44769 Z= 0.290 Chirality : 0.041 0.161 4911 Planarity : 0.004 0.063 5144 Dihedral : 18.624 172.517 6133 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.25 % Allowed : 14.98 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3416 helix: 0.88 (0.17), residues: 1043 sheet: 0.03 (0.19), residues: 794 loop : -1.42 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 93 TYR 0.019 0.001 TYR X 261 PHE 0.020 0.001 PHE T 354 TRP 0.013 0.001 TRP P 204 HIS 0.010 0.001 HIS W 392 Details of bonding type rmsd covalent geometry : bond 0.00326 (32487) covalent geometry : angle 0.54529 (44769) hydrogen bonds : bond 0.03755 ( 1196) hydrogen bonds : angle 4.59831 ( 3291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 310 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7312 (mm-30) REVERT: S 392 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7975 (m90) REVERT: T 51 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7189 (tp40) REVERT: T 171 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6698 (mp) REVERT: T 188 LYS cc_start: 0.5907 (mmtt) cc_final: 0.5546 (mtpm) REVERT: T 235 ASN cc_start: 0.6669 (t0) cc_final: 0.6170 (p0) REVERT: T 237 LYS cc_start: 0.7579 (mttp) cc_final: 0.7369 (mptp) REVERT: T 333 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7472 (tm-30) REVERT: O 314 LYS cc_start: 0.8119 (tppt) cc_final: 0.7764 (tptm) REVERT: O 392 HIS cc_start: 0.8364 (t-90) cc_final: 0.8129 (t-90) REVERT: P 16 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: P 43 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7773 (pt) REVERT: P 47 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6544 (ttt) REVERT: P 55 ARG cc_start: 0.7273 (mmm160) cc_final: 0.6350 (mtm110) REVERT: P 68 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7890 (tppt) REVERT: P 261 TYR cc_start: 0.7166 (t80) cc_final: 0.6668 (t80) REVERT: P 307 LYS cc_start: 0.8213 (ptpp) cc_final: 0.7737 (mmtm) REVERT: P 402 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6768 (mmm) REVERT: Y 224 GLU cc_start: 0.7374 (pt0) cc_final: 0.6764 (pm20) REVERT: Y 312 GLU cc_start: 0.6727 (mp0) cc_final: 0.6363 (mp0) REVERT: U 95 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: U 114 LYS cc_start: 0.8685 (mptt) cc_final: 0.8352 (mtmt) REVERT: U 226 ILE cc_start: 0.7820 (mp) cc_final: 0.7531 (tp) REVERT: U 268 GLU cc_start: 0.8307 (tt0) cc_final: 0.8097 (pt0) REVERT: U 449 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: X 9 GLN cc_start: 0.7163 (mt0) cc_final: 0.6697 (tt0) REVERT: X 168 MET cc_start: 0.9028 (mtp) cc_final: 0.8545 (mtm) REVERT: X 171 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7970 (mp) REVERT: X 207 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7329 (m110) REVERT: X 231 VAL cc_start: 0.6928 (t) cc_final: 0.6703 (m) outliers start: 66 outliers final: 33 residues processed: 272 average time/residue: 0.7522 time to fit residues: 239.5609 Evaluate side-chains 262 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 376 LEU Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 171 LEU Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 377 MET Chi-restraints excluded: chain T residue 402 MET Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain Y residue 412 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain U residue 449 GLN Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 207 ASN Chi-restraints excluded: chain X residue 222 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 357 optimal weight: 0.5980 chunk 288 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 349 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** W 326 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.132050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100546 restraints weight = 48626.272| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.92 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32487 Z= 0.164 Angle : 0.564 11.761 44769 Z= 0.300 Chirality : 0.042 0.169 4911 Planarity : 0.004 0.061 5144 Dihedral : 18.613 172.973 6133 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.46 % Allowed : 15.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3416 helix: 0.90 (0.16), residues: 1046 sheet: -0.06 (0.19), residues: 784 loop : -1.39 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 93 TYR 0.021 0.001 TYR X 261 PHE 0.025 0.002 PHE T 354 TRP 0.010 0.001 TRP Y 212 HIS 0.006 0.001 HIS X 215 Details of bonding type rmsd covalent geometry : bond 0.00382 (32487) covalent geometry : angle 0.56399 (44769) hydrogen bonds : bond 0.03897 ( 1196) hydrogen bonds : angle 4.65669 ( 3291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 109 LEU cc_start: 0.7905 (mp) cc_final: 0.7695 (mm) REVERT: S 310 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7337 (mm-30) REVERT: S 392 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7952 (m90) REVERT: T 51 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7137 (tp40) REVERT: T 171 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6714 (mp) REVERT: T 188 LYS cc_start: 0.5892 (mmtt) cc_final: 0.5529 (mtpm) REVERT: T 235 ASN cc_start: 0.6755 (t0) cc_final: 0.6243 (p0) REVERT: O 38 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.7853 (tt) REVERT: O 58 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8083 (mttp) REVERT: O 314 LYS cc_start: 0.8095 (tppt) cc_final: 0.7719 (tptm) REVERT: O 392 HIS cc_start: 0.8354 (t-90) cc_final: 0.8115 (t-90) REVERT: P 16 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: P 43 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7737 (pt) REVERT: P 47 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6516 (ttt) REVERT: P 55 ARG cc_start: 0.7306 (mmm160) cc_final: 0.6336 (mtm110) REVERT: P 68 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7911 (tppt) REVERT: P 261 TYR cc_start: 0.7177 (t80) cc_final: 0.6635 (t80) REVERT: P 307 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7742 (mmtm) REVERT: P 402 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6737 (mmm) REVERT: W 270 ASP cc_start: 0.7907 (p0) cc_final: 0.7063 (t0) REVERT: Y 224 GLU cc_start: 0.7426 (pt0) cc_final: 0.6851 (pp20) REVERT: Y 247 GLU cc_start: 0.6508 (mt-10) cc_final: 0.5689 (mm-30) REVERT: Y 297 LYS cc_start: 0.6914 (mptt) cc_final: 0.5724 (tmtt) REVERT: Y 312 GLU cc_start: 0.6715 (mp0) cc_final: 0.6357 (mp0) REVERT: U 95 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: U 114 LYS cc_start: 0.8675 (mptt) cc_final: 0.8301 (mtmt) REVERT: U 226 ILE cc_start: 0.7782 (mp) cc_final: 0.7515 (tp) REVERT: U 268 GLU cc_start: 0.8302 (tt0) cc_final: 0.8083 (pt0) REVERT: U 449 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: X 9 GLN cc_start: 0.7144 (mt0) cc_final: 0.6658 (tt0) REVERT: X 207 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7321 (m110) REVERT: X 231 VAL cc_start: 0.7003 (t) cc_final: 0.6802 (m) outliers start: 72 outliers final: 41 residues processed: 277 average time/residue: 0.7228 time to fit residues: 234.2814 Evaluate side-chains 273 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 376 LEU Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 171 LEU Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 252 SER Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 377 MET Chi-restraints excluded: chain T residue 402 MET Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 47 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 257 GLN Chi-restraints excluded: chain P residue 402 MET Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 400 TYR Chi-restraints excluded: chain Y residue 412 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 40 ASP Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain U residue 449 GLN Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 207 ASN Chi-restraints excluded: chain X residue 222 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 142 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** W 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097583 restraints weight = 48702.888| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.92 r_work: 0.3188 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 32487 Z= 0.288 Angle : 0.681 12.050 44769 Z= 0.360 Chirality : 0.047 0.208 4911 Planarity : 0.006 0.073 5144 Dihedral : 18.798 171.180 6133 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.53 % Allowed : 15.39 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3416 helix: 0.61 (0.16), residues: 1042 sheet: -0.15 (0.18), residues: 801 loop : -1.52 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 93 TYR 0.032 0.002 TYR X 261 PHE 0.033 0.002 PHE T 354 TRP 0.021 0.002 TRP X 212 HIS 0.008 0.001 HIS X 321 Details of bonding type rmsd covalent geometry : bond 0.00683 (32487) covalent geometry : angle 0.68134 (44769) hydrogen bonds : bond 0.04738 ( 1196) hydrogen bonds : angle 4.97959 ( 3291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 222 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: S 310 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7412 (mm-30) REVERT: T 51 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7247 (tp40) REVERT: T 188 LYS cc_start: 0.5882 (mmtt) cc_final: 0.5391 (mtpm) REVERT: T 235 ASN cc_start: 0.6994 (t0) cc_final: 0.6285 (p0) REVERT: T 237 LYS cc_start: 0.7153 (mptp) cc_final: 0.6363 (mtpt) REVERT: O 38 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8185 (tt) REVERT: O 58 LYS cc_start: 0.8490 (mtmt) cc_final: 0.7980 (mttp) REVERT: O 314 LYS cc_start: 0.8124 (tppt) cc_final: 0.7725 (tptm) REVERT: P 16 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: P 43 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (pt) REVERT: P 55 ARG cc_start: 0.7362 (mmm160) cc_final: 0.6365 (mtm110) REVERT: P 68 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7970 (tppt) REVERT: P 261 TYR cc_start: 0.7261 (t80) cc_final: 0.6653 (t80) REVERT: P 307 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7637 (mmtm) REVERT: W 87 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8089 (mp-120) REVERT: W 270 ASP cc_start: 0.7908 (p0) cc_final: 0.7106 (t0) REVERT: Y 224 GLU cc_start: 0.7462 (pt0) cc_final: 0.6938 (pp20) REVERT: Y 247 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6187 (mp0) REVERT: Y 297 LYS cc_start: 0.6846 (mptt) cc_final: 0.5716 (tmtt) REVERT: Y 312 GLU cc_start: 0.6741 (mp0) cc_final: 0.6459 (mp0) REVERT: U 95 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: U 114 LYS cc_start: 0.8784 (mptt) cc_final: 0.8368 (mtmt) REVERT: U 226 ILE cc_start: 0.7845 (mp) cc_final: 0.7620 (tp) REVERT: U 449 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: X 9 GLN cc_start: 0.7176 (mt0) cc_final: 0.6686 (tt0) REVERT: X 168 MET cc_start: 0.9064 (mtp) cc_final: 0.8632 (mtm) REVERT: X 207 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7336 (m110) outliers start: 74 outliers final: 36 residues processed: 274 average time/residue: 0.6902 time to fit residues: 220.7807 Evaluate side-chains 257 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 253 GLU Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 444 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 51 GLN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 87 GLN Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain U residue 449 GLN Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 207 ASN Chi-restraints excluded: chain X residue 222 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 125 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100932 restraints weight = 48483.841| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.90 r_work: 0.3244 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32487 Z= 0.143 Angle : 0.572 11.711 44769 Z= 0.304 Chirality : 0.041 0.185 4911 Planarity : 0.004 0.069 5144 Dihedral : 18.608 173.327 6133 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.74 % Allowed : 16.21 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3416 helix: 0.94 (0.16), residues: 1042 sheet: -0.07 (0.19), residues: 795 loop : -1.39 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG T 218 TYR 0.020 0.001 TYR X 261 PHE 0.024 0.001 PHE T 354 TRP 0.015 0.001 TRP X 212 HIS 0.007 0.001 HIS X 215 Details of bonding type rmsd covalent geometry : bond 0.00325 (32487) covalent geometry : angle 0.57152 (44769) hydrogen bonds : bond 0.03799 ( 1196) hydrogen bonds : angle 4.69987 ( 3291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 109 LEU cc_start: 0.7996 (mp) cc_final: 0.7776 (mm) REVERT: S 310 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7386 (mm-30) REVERT: S 392 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.7965 (m90) REVERT: T 56 MET cc_start: 0.8677 (mmt) cc_final: 0.8032 (mmt) REVERT: T 188 LYS cc_start: 0.5852 (mmtt) cc_final: 0.5343 (mtpm) REVERT: T 235 ASN cc_start: 0.6967 (t0) cc_final: 0.6279 (p0) REVERT: T 237 LYS cc_start: 0.7149 (mptp) cc_final: 0.6340 (mtpt) REVERT: T 306 PHE cc_start: 0.7168 (m-80) cc_final: 0.6856 (m-80) REVERT: T 311 ASP cc_start: 0.5897 (t70) cc_final: 0.5404 (p0) REVERT: O 58 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8123 (mttp) REVERT: O 208 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8388 (pptt) REVERT: O 314 LYS cc_start: 0.8099 (tppt) cc_final: 0.7812 (tptm) REVERT: P 16 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: P 43 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7758 (pt) REVERT: P 55 ARG cc_start: 0.7377 (mmm160) cc_final: 0.6381 (mtm110) REVERT: P 68 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7972 (tppt) REVERT: W 270 ASP cc_start: 0.7878 (p0) cc_final: 0.7130 (t0) REVERT: Y 224 GLU cc_start: 0.7443 (pt0) cc_final: 0.6889 (pp20) REVERT: Y 247 GLU cc_start: 0.6447 (mt-10) cc_final: 0.6127 (mp0) REVERT: Y 297 LYS cc_start: 0.6883 (mptt) cc_final: 0.5749 (tmtt) REVERT: Y 312 GLU cc_start: 0.6741 (mp0) cc_final: 0.6462 (mp0) REVERT: U 95 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: U 114 LYS cc_start: 0.8725 (mptt) cc_final: 0.8352 (mtmt) REVERT: U 226 ILE cc_start: 0.7802 (mp) cc_final: 0.7531 (tp) REVERT: X 9 GLN cc_start: 0.7154 (mt0) cc_final: 0.6628 (tt0) REVERT: X 168 MET cc_start: 0.9046 (mtp) cc_final: 0.8656 (mtp) REVERT: X 207 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7374 (m110) outliers start: 51 outliers final: 32 residues processed: 262 average time/residue: 0.7194 time to fit residues: 220.7026 Evaluate side-chains 255 residues out of total 2935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 231 TRP Chi-restraints excluded: chain S residue 253 GLU Chi-restraints excluded: chain S residue 300 SER Chi-restraints excluded: chain S residue 392 HIS Chi-restraints excluded: chain T residue 298 THR Chi-restraints excluded: chain T residue 366 ASP Chi-restraints excluded: chain T residue 402 MET Chi-restraints excluded: chain T residue 412 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 231 TRP Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 16 GLU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 231 TRP Chi-restraints excluded: chain W residue 476 VAL Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 285 VAL Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 231 TRP Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 165 LEU Chi-restraints excluded: chain X residue 207 ASN Chi-restraints excluded: chain X residue 222 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 267 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 ASN O 86 ASN ** O 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** W 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 213 GLN ** W 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 ASN U 424 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104406 restraints weight = 48360.797| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.13 r_work: 0.3269 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32487 Z= 0.115 Angle : 0.533 11.472 44769 Z= 0.282 Chirality : 0.040 0.162 4911 Planarity : 0.004 0.073 5144 Dihedral : 18.431 176.417 6133 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.30 % Allowed : 16.96 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3416 helix: 1.15 (0.17), residues: 1048 sheet: 0.05 (0.19), residues: 791 loop : -1.23 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG T 218 TYR 0.018 0.001 TYR P 291 PHE 0.021 0.001 PHE T 354 TRP 0.011 0.001 TRP P 204 HIS 0.007 0.001 HIS X 215 Details of bonding type rmsd covalent geometry : bond 0.00260 (32487) covalent geometry : angle 0.53311 (44769) hydrogen bonds : bond 0.03365 ( 1196) hydrogen bonds : angle 4.46582 ( 3291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11986.43 seconds wall clock time: 204 minutes 38.01 seconds (12278.01 seconds total)