Starting phenix.real_space_refine on Mon Jul 6 12:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.map" model { file = "/net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb3_52984/07_2026/9qb3_52984.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 366 5.49 5 S 172 5.16 5 C 20610 2.51 5 N 6142 2.21 5 O 7432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 214 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34722 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3129 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "E" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "G" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2792 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain: "I" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "J" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "K" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2724 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 23, 'TRANS': 324} Chain breaks: 3 Chain: "c" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3129 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Chain: "d" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "e" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "f" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "g" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2792 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain: "h" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain: "i" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "j" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "k" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2724 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 23, 'TRANS': 324} Chain breaks: 3 Chain: "B" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3980 Inner-chain residues flagged as termini: ['pdbres=" U B 195 "', 'pdbres=" G B 322 "', 'pdbres=" G B 362 "'] Classifications: {'RNA': 186} Modifications used: {'5*END': 3, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 83, 'rna3p_pyr': 77} Link IDs: {'rna2p': 22, 'rna3p': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "b" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3980 Inner-chain residues flagged as termini: ['pdbres=" U b 195 "', 'pdbres=" G b 322 "', 'pdbres=" G b 362 "'] Classifications: {'RNA': 186} Modifications used: {'5*END': 3, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 83, 'rna3p_pyr': 77} Link IDs: {'rna2p': 22, 'rna3p': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 7.21, per 1000 atoms: 0.21 Number of scatterers: 34722 At special positions: 0 Unit cell: (162.027, 166.263, 153.555, 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 172 16.00 P 366 15.00 O 7432 8.00 N 6142 7.00 C 20610 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 36 sheets defined 30.4% alpha, 20.4% beta 122 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.649A pdb=" N HIS C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.777A pdb=" N ARG C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 138 through 141 removed outlier: 3.614A pdb=" N ARG C 141 " --> pdb=" O ARG C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 165 through 176 removed outlier: 4.025A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.934A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.551A pdb=" N THR C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.952A pdb=" N PHE D 138 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.735A pdb=" N LEU E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 28' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 40 through 57 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 93 through 101 removed outlier: 3.745A pdb=" N ARG E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.517A pdb=" N ARG F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.565A pdb=" N GLN F 59 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.740A pdb=" N ARG G 81 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 138 through 141 Processing helix chain 'G' and resid 142 through 148 Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.817A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 238 Processing helix chain 'G' and resid 263 through 277 Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 290 through 294 removed outlier: 3.943A pdb=" N THR G 294 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.531A pdb=" N VAL G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 358 Processing helix chain 'G' and resid 383 through 395 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.615A pdb=" N LYS H 94 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.905A pdb=" N PHE H 138 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 157 Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 40 through 57 Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.503A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.536A pdb=" N VAL I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 102 removed outlier: 3.597A pdb=" N ARG I 101 " --> pdb=" O MET I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.535A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 135 through 148 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.506A pdb=" N GLN J 59 " --> pdb=" O MET J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 4.016A pdb=" N GLN K 167 " --> pdb=" O PHE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 4.455A pdb=" N TYR K 203 " --> pdb=" O PRO K 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 34 removed outlier: 3.649A pdb=" N HIS c 32 " --> pdb=" O ALA c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 57 Processing helix chain 'c' and resid 77 through 81 removed outlier: 3.776A pdb=" N ARG c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 89 Processing helix chain 'c' and resid 101 through 113 Processing helix chain 'c' and resid 138 through 141 removed outlier: 3.614A pdb=" N ARG c 141 " --> pdb=" O ARG c 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 138 through 141' Processing helix chain 'c' and resid 142 through 148 Processing helix chain 'c' and resid 165 through 176 removed outlier: 4.026A pdb=" N LEU c 169 " --> pdb=" O GLY c 165 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 238 Processing helix chain 'c' and resid 262 through 277 Processing helix chain 'c' and resid 281 through 286 Processing helix chain 'c' and resid 290 through 294 removed outlier: 3.934A pdb=" N THR c 294 " --> pdb=" O LYS c 291 " (cutoff:3.500A) Processing helix chain 'c' and resid 305 through 311 Processing helix chain 'c' and resid 351 through 358 removed outlier: 3.551A pdb=" N THR c 357 " --> pdb=" O ALA c 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 383 through 395 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'd' and resid 90 through 94 Processing helix chain 'd' and resid 134 through 138 removed outlier: 3.952A pdb=" N PHE d 138 " --> pdb=" O ALA d 135 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 149 No H-bonds generated for 'chain 'd' and resid 147 through 149' Processing helix chain 'd' and resid 153 through 157 Processing helix chain 'e' and resid 24 through 28 removed outlier: 3.736A pdb=" N LEU e 28 " --> pdb=" O TYR e 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 28' Processing helix chain 'e' and resid 29 through 31 No H-bonds generated for 'chain 'e' and resid 29 through 31' Processing helix chain 'e' and resid 40 through 57 Processing helix chain 'e' and resid 63 through 74 Processing helix chain 'e' and resid 87 through 91 Processing helix chain 'e' and resid 93 through 101 removed outlier: 3.745A pdb=" N ARG e 101 " --> pdb=" O MET e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 118 Processing helix chain 'e' and resid 135 through 148 Processing helix chain 'f' and resid 41 through 52 removed outlier: 3.517A pdb=" N ARG f 51 " --> pdb=" O THR f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 59 removed outlier: 3.565A pdb=" N GLN f 59 " --> pdb=" O MET f 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 57 Processing helix chain 'g' and resid 58 through 62 Processing helix chain 'g' and resid 77 through 81 removed outlier: 3.740A pdb=" N ARG g 81 " --> pdb=" O PRO g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 89 Processing helix chain 'g' and resid 101 through 113 Processing helix chain 'g' and resid 138 through 141 Processing helix chain 'g' and resid 142 through 148 Processing helix chain 'g' and resid 165 through 176 removed outlier: 3.817A pdb=" N LEU g 169 " --> pdb=" O GLY g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 225 through 238 Processing helix chain 'g' and resid 263 through 277 Processing helix chain 'g' and resid 281 through 286 Processing helix chain 'g' and resid 290 through 294 removed outlier: 3.943A pdb=" N THR g 294 " --> pdb=" O LYS g 291 " (cutoff:3.500A) Processing helix chain 'g' and resid 302 through 311 removed outlier: 3.530A pdb=" N VAL g 306 " --> pdb=" O LYS g 302 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA g 308 " --> pdb=" O SER g 304 " (cutoff:3.500A) Processing helix chain 'g' and resid 351 through 358 Processing helix chain 'g' and resid 383 through 395 Processing helix chain 'h' and resid 90 through 94 removed outlier: 3.616A pdb=" N LYS h 94 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 134 through 138 removed outlier: 3.904A pdb=" N PHE h 138 " --> pdb=" O ALA h 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 153 through 157 Processing helix chain 'i' and resid 24 through 28 Processing helix chain 'i' and resid 29 through 31 No H-bonds generated for 'chain 'i' and resid 29 through 31' Processing helix chain 'i' and resid 40 through 57 Processing helix chain 'i' and resid 63 through 74 removed outlier: 3.505A pdb=" N LYS i 69 " --> pdb=" O LYS i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 91 removed outlier: 3.536A pdb=" N VAL i 90 " --> pdb=" O PRO i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 102 removed outlier: 3.597A pdb=" N ARG i 101 " --> pdb=" O MET i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 118 removed outlier: 3.535A pdb=" N ALA i 118 " --> pdb=" O LEU i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 134 No H-bonds generated for 'chain 'i' and resid 132 through 134' Processing helix chain 'i' and resid 135 through 148 Processing helix chain 'j' and resid 41 through 52 Processing helix chain 'j' and resid 55 through 59 removed outlier: 3.506A pdb=" N GLN j 59 " --> pdb=" O MET j 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 163 through 167 removed outlier: 4.015A pdb=" N GLN k 167 " --> pdb=" O PHE k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 199 through 204 removed outlier: 4.456A pdb=" N TYR k 203 " --> pdb=" O PRO k 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.765A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 297 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE C 343 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL C 369 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 345 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 315 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 96 current: chain 'C' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 136 current: chain 'C' and resid 195 through 208 removed outlier: 5.456A pdb=" N SER C 202 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER C 219 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET C 204 " --> pdb=" O TRP C 217 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 217 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 206 " --> pdb=" O ILE C 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 213 through 220 current: chain 'C' and resid 254 through 255 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 254 through 255 current: chain 'D' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 88 current: chain 'D' and resid 109 through 119 removed outlier: 5.330A pdb=" N VAL D 113 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS D 128 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 115 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.765A pdb=" N VAL G 300 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR G 323 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG G 298 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS G 297 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE G 336 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE G 343 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL G 369 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET G 345 " --> pdb=" O LYS G 367 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE G 315 " --> pdb=" O VAL G 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 96 current: chain 'G' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 129 through 136 current: chain 'G' and resid 195 through 208 removed outlier: 5.429A pdb=" N SER G 202 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER G 219 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET G 204 " --> pdb=" O TRP G 217 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP G 217 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 206 " --> pdb=" O ILE G 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 220 current: chain 'G' and resid 254 through 255 Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 79 removed outlier: 4.452A pdb=" N VAL H 85 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE H 123 " --> pdb=" O CYS H 88 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 119 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU H 115 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS H 128 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL H 113 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'K' and resid 155 through 160 removed outlier: 3.581A pdb=" N LEU K 516 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY K 159 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU K 514 " --> pdb=" O GLY K 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 172 through 177 removed outlier: 4.421A pdb=" N GLY K 174 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN K 187 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER K 188 " --> pdb=" O ILE K 192 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU K 218 " --> pdb=" O ILE K 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 226 through 231 removed outlier: 3.690A pdb=" N ASP K 228 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE K 254 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER K 267 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE K 256 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.674A pdb=" N THR K 299 " --> pdb=" O PHE K 296 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 328 through 333 removed outlier: 3.597A pdb=" N ALA K 361 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA K 353 " --> pdb=" O PRO K 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 370 through 375 removed outlier: 4.793A pdb=" N ALA K 386 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU K 391 " --> pdb=" O ALA K 386 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP K 405 " --> pdb=" O CYS K 394 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.570A pdb=" N VAL K 437 " --> pdb=" O SER K 456 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER K 456 " --> pdb=" O VAL K 437 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL K 439 " --> pdb=" O VAL K 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 63 through 64 removed outlier: 6.767A pdb=" N VAL c 300 " --> pdb=" O LEU c 321 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR c 323 " --> pdb=" O ARG c 298 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG c 298 " --> pdb=" O TYR c 323 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS c 297 " --> pdb=" O GLU c 332 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE c 343 " --> pdb=" O VAL c 369 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL c 369 " --> pdb=" O ILE c 343 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET c 345 " --> pdb=" O LYS c 367 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE c 315 " --> pdb=" O VAL c 363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 90 through 96 current: chain 'c' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 129 through 136 current: chain 'c' and resid 195 through 208 removed outlier: 5.457A pdb=" N SER c 202 " --> pdb=" O SER c 219 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER c 219 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N MET c 204 " --> pdb=" O TRP c 217 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP c 217 " --> pdb=" O MET c 204 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU c 206 " --> pdb=" O ILE c 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 213 through 220 current: chain 'c' and resid 254 through 255 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 254 through 255 current: chain 'd' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 83 through 88 current: chain 'd' and resid 109 through 119 removed outlier: 5.329A pdb=" N VAL d 113 " --> pdb=" O LYS d 128 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS d 128 " --> pdb=" O VAL d 113 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU d 115 " --> pdb=" O SER d 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 95 through 96 Processing sheet with id=AC4, first strand: chain 'e' and resid 61 through 62 Processing sheet with id=AC5, first strand: chain 'f' and resid 13 through 16 Processing sheet with id=AC6, first strand: chain 'g' and resid 63 through 64 removed outlier: 6.766A pdb=" N VAL g 300 " --> pdb=" O LEU g 321 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR g 323 " --> pdb=" O ARG g 298 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG g 298 " --> pdb=" O TYR g 323 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS g 297 " --> pdb=" O VAL g 334 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE g 336 " --> pdb=" O LYS g 297 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU g 299 " --> pdb=" O ILE g 336 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE g 343 " --> pdb=" O VAL g 369 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL g 369 " --> pdb=" O ILE g 343 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET g 345 " --> pdb=" O LYS g 367 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE g 315 " --> pdb=" O VAL g 363 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 90 through 96 current: chain 'g' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 129 through 136 current: chain 'g' and resid 195 through 208 removed outlier: 5.429A pdb=" N SER g 202 " --> pdb=" O SER g 219 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER g 219 " --> pdb=" O SER g 202 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET g 204 " --> pdb=" O TRP g 217 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP g 217 " --> pdb=" O MET g 204 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU g 206 " --> pdb=" O ILE g 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 213 through 220 current: chain 'g' and resid 254 through 255 Processing sheet with id=AC8, first strand: chain 'h' and resid 71 through 79 removed outlier: 4.452A pdb=" N VAL h 85 " --> pdb=" O LEU h 77 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE h 123 " --> pdb=" O CYS h 88 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN h 119 " --> pdb=" O ASP h 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU h 115 " --> pdb=" O SER h 126 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS h 128 " --> pdb=" O VAL h 113 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL h 113 " --> pdb=" O LYS h 128 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE h 144 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 95 through 96 Processing sheet with id=AD1, first strand: chain 'i' and resid 60 through 61 Processing sheet with id=AD2, first strand: chain 'j' and resid 13 through 16 Processing sheet with id=AD3, first strand: chain 'k' and resid 155 through 160 removed outlier: 3.581A pdb=" N LEU k 516 " --> pdb=" O LEU k 157 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY k 159 " --> pdb=" O LEU k 514 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU k 514 " --> pdb=" O GLY k 159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 172 through 177 removed outlier: 4.423A pdb=" N GLY k 174 " --> pdb=" O ASN k 187 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN k 187 " --> pdb=" O GLY k 174 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER k 188 " --> pdb=" O ILE k 192 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE k 192 " --> pdb=" O SER k 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU k 218 " --> pdb=" O ILE k 195 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 226 through 231 removed outlier: 3.690A pdb=" N ASP k 228 " --> pdb=" O SER k 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE k 254 " --> pdb=" O SER k 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER k 267 " --> pdb=" O ILE k 254 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE k 256 " --> pdb=" O ARG k 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 284 through 285 removed outlier: 3.674A pdb=" N THR k 299 " --> pdb=" O PHE k 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 328 through 333 removed outlier: 3.596A pdb=" N ALA k 361 " --> pdb=" O LEU k 351 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA k 353 " --> pdb=" O PRO k 359 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'k' and resid 370 through 375 removed outlier: 4.793A pdb=" N ALA k 386 " --> pdb=" O GLU k 391 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU k 391 " --> pdb=" O ALA k 386 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP k 405 " --> pdb=" O CYS k 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'k' and resid 419 through 421 removed outlier: 6.569A pdb=" N VAL k 437 " --> pdb=" O SER k 456 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER k 456 " --> pdb=" O VAL k 437 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL k 439 " --> pdb=" O VAL k 454 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5925 1.33 - 1.45: 11284 1.45 - 1.58: 18061 1.58 - 1.70: 724 1.70 - 1.82: 250 Bond restraints: 36244 Sorted by residual: bond pdb=" O5' G b 339 " pdb=" C5' G b 339 " ideal model delta sigma weight residual 1.420 1.466 -0.046 1.50e-02 4.44e+03 9.56e+00 bond pdb=" O5' G B 339 " pdb=" C5' G B 339 " ideal model delta sigma weight residual 1.420 1.465 -0.045 1.50e-02 4.44e+03 9.17e+00 bond pdb=" N9 G B 345 " pdb=" C8 G B 345 " ideal model delta sigma weight residual 1.374 1.395 -0.021 7.00e-03 2.04e+04 8.92e+00 bond pdb=" CE1 HIS g 120 " pdb=" NE2 HIS g 120 " ideal model delta sigma weight residual 1.321 1.291 0.030 1.00e-02 1.00e+04 8.83e+00 bond pdb=" CE1 HIS G 120 " pdb=" NE2 HIS G 120 " ideal model delta sigma weight residual 1.321 1.291 0.030 1.00e-02 1.00e+04 8.76e+00 ... (remaining 36239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 48420 2.66 - 5.31: 2356 5.31 - 7.97: 58 7.97 - 10.63: 2 10.63 - 13.28: 2 Bond angle restraints: 50838 Sorted by residual: angle pdb=" C2' G b 345 " pdb=" C1' G b 345 " pdb=" N9 G b 345 " ideal model delta sigma weight residual 112.00 125.28 -13.28 1.50e+00 4.44e-01 7.84e+01 angle pdb=" C2' G B 345 " pdb=" C1' G B 345 " pdb=" N9 G B 345 " ideal model delta sigma weight residual 112.00 125.27 -13.27 1.50e+00 4.44e-01 7.83e+01 angle pdb=" C1' G B 345 " pdb=" N9 G B 345 " pdb=" C8 G B 345 " ideal model delta sigma weight residual 127.00 135.45 -8.45 1.30e+00 5.92e-01 4.23e+01 angle pdb=" C1' G b 345 " pdb=" N9 G b 345 " pdb=" C8 G b 345 " ideal model delta sigma weight residual 127.00 135.42 -8.42 1.30e+00 5.92e-01 4.20e+01 angle pdb=" C8 G B 345 " pdb=" N9 G B 345 " pdb=" C4 G B 345 " ideal model delta sigma weight residual 106.40 104.22 2.18 4.00e-01 6.25e+00 2.98e+01 ... (remaining 50833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 20462 20.34 - 40.69: 1172 40.69 - 61.03: 566 61.03 - 81.38: 478 81.38 - 101.72: 6 Dihedral angle restraints: 22684 sinusoidal: 12942 harmonic: 9742 Sorted by residual: dihedral pdb=" C5' G B 450 " pdb=" C4' G B 450 " pdb=" C3' G B 450 " pdb=" O3' G B 450 " ideal model delta sinusoidal sigma weight residual 147.00 108.31 38.69 1 8.00e+00 1.56e-02 3.29e+01 dihedral pdb=" C5' G b 450 " pdb=" C4' G b 450 " pdb=" C3' G b 450 " pdb=" O3' G b 450 " ideal model delta sinusoidal sigma weight residual 147.00 108.33 38.67 1 8.00e+00 1.56e-02 3.29e+01 dihedral pdb=" CA TYR k 345 " pdb=" C TYR k 345 " pdb=" N GLY k 346 " pdb=" CA GLY k 346 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 22681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 5090 0.127 - 0.254: 826 0.254 - 0.380: 12 0.380 - 0.507: 4 0.507 - 0.634: 6 Chirality restraints: 5938 Sorted by residual: chirality pdb=" C1' G b 345 " pdb=" O4' G b 345 " pdb=" C2' G b 345 " pdb=" N9 G b 345 " both_signs ideal model delta sigma weight residual False 2.46 1.82 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C1' G B 345 " pdb=" O4' G B 345 " pdb=" C2' G B 345 " pdb=" N9 G B 345 " both_signs ideal model delta sigma weight residual False 2.46 1.82 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P C B 18 " pdb=" OP1 C B 18 " pdb=" OP2 C B 18 " pdb=" O5' C B 18 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 8.94e+00 ... (remaining 5935 not shown) Planarity restraints: 5096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A b 374 " -0.027 2.00e-02 2.50e+03 3.07e-02 2.59e+01 pdb=" N9 A b 374 " -0.008 2.00e-02 2.50e+03 pdb=" C8 A b 374 " 0.023 2.00e-02 2.50e+03 pdb=" N7 A b 374 " 0.052 2.00e-02 2.50e+03 pdb=" C5 A b 374 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A b 374 " -0.020 2.00e-02 2.50e+03 pdb=" N6 A b 374 " -0.046 2.00e-02 2.50e+03 pdb=" N1 A b 374 " 0.025 2.00e-02 2.50e+03 pdb=" C2 A b 374 " 0.035 2.00e-02 2.50e+03 pdb=" N3 A b 374 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A b 374 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 374 " 0.027 2.00e-02 2.50e+03 3.06e-02 2.58e+01 pdb=" N9 A B 374 " 0.008 2.00e-02 2.50e+03 pdb=" C8 A B 374 " -0.021 2.00e-02 2.50e+03 pdb=" N7 A B 374 " -0.052 2.00e-02 2.50e+03 pdb=" C5 A B 374 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A B 374 " 0.021 2.00e-02 2.50e+03 pdb=" N6 A B 374 " 0.046 2.00e-02 2.50e+03 pdb=" N1 A B 374 " -0.024 2.00e-02 2.50e+03 pdb=" C2 A B 374 " -0.035 2.00e-02 2.50e+03 pdb=" N3 A B 374 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 374 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U b 418 " 0.052 2.00e-02 2.50e+03 2.54e-02 1.45e+01 pdb=" N1 U b 418 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U b 418 " -0.020 2.00e-02 2.50e+03 pdb=" O2 U b 418 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U b 418 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U b 418 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U b 418 " 0.023 2.00e-02 2.50e+03 pdb=" C5 U b 418 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U b 418 " -0.028 2.00e-02 2.50e+03 ... (remaining 5093 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2110 2.75 - 3.29: 32341 3.29 - 3.82: 56902 3.82 - 4.36: 78179 4.36 - 4.90: 118310 Nonbonded interactions: 287842 Sorted by model distance: nonbonded pdb=" NZ LYS H 94 " pdb=" OE1 GLU h 68 " model vdw 2.211 3.120 nonbonded pdb=" OE1 GLU H 68 " pdb=" NZ LYS h 94 " model vdw 2.215 3.120 nonbonded pdb=" O GLY G 312 " pdb=" O2' G B 381 " model vdw 2.244 3.040 nonbonded pdb=" O GLY g 312 " pdb=" O2' G b 381 " model vdw 2.250 3.040 nonbonded pdb=" O ARG I 62 " pdb=" O VAL I 126 " model vdw 2.297 3.040 ... (remaining 287837 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and resid 43 through 395) selection = (chain 'G' and (resid 43 through 186 or resid 192 through 395)) selection = (chain 'c' and resid 43 through 395) selection = (chain 'g' and (resid 43 through 186 or resid 192 through 395)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 66 through 159) selection = chain 'd' selection = (chain 'h' and resid 66 through 159) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'e' selection = chain 'i' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'f' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 35.760 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.009 0.050 36244 Z= 0.585 Angle : 1.242 13.283 50838 Z= 0.854 Chirality : 0.087 0.634 5938 Planarity : 0.009 0.130 5096 Dihedral : 18.206 101.721 16408 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.27 % Allowed : 1.39 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.64 (0.13), residues: 3296 helix: -1.44 (0.14), residues: 768 sheet: -1.91 (0.18), residues: 610 loop : -0.54 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG G 111 TYR 0.029 0.005 TYR j 15 PHE 0.024 0.004 PHE i 70 TRP 0.046 0.005 TRP G 380 HIS 0.025 0.004 HIS G 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.58 (36244) covalent geometry : angle 1.24189 / 0.85 (50838) hydrogen bonds : bond 0.21725 / 14.59 ( 1173) hydrogen bonds : angle 7.81080 / 5.29 ( 2839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 764 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7357 (mmm160) REVERT: C 260 MET cc_start: 0.9487 (ttp) cc_final: 0.9277 (ttm) REVERT: C 350 MET cc_start: 0.9046 (mtt) cc_final: 0.8752 (mtt) REVERT: D 78 HIS cc_start: 0.9004 (p-80) cc_final: 0.8756 (p90) REVERT: D 82 ASP cc_start: 0.9488 (m-30) cc_final: 0.9288 (t0) REVERT: D 87 LYS cc_start: 0.8643 (tttt) cc_final: 0.8317 (tptt) REVERT: D 113 VAL cc_start: 0.8840 (t) cc_final: 0.8561 (m) REVERT: D 120 LEU cc_start: 0.8794 (mp) cc_final: 0.8072 (pp) REVERT: D 125 PHE cc_start: 0.7698 (p90) cc_final: 0.7246 (p90) REVERT: E 59 GLN cc_start: 0.8202 (mm110) cc_final: 0.7721 (mt0) REVERT: E 78 ILE cc_start: 0.8801 (tt) cc_final: 0.8572 (tp) REVERT: E 79 MET cc_start: 0.9460 (ttm) cc_final: 0.9134 (mpp) REVERT: E 81 LEU cc_start: 0.9259 (mt) cc_final: 0.9019 (mp) REVERT: E 99 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9224 (mt-10) REVERT: E 105 TYR cc_start: 0.9509 (p90) cc_final: 0.8957 (p90) REVERT: E 113 ASP cc_start: 0.9249 (m-30) cc_final: 0.8820 (t0) REVERT: E 128 MET cc_start: 0.8660 (ttp) cc_final: 0.7789 (tpp) REVERT: E 141 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9403 (mt-10) REVERT: F 2 PHE cc_start: 0.8624 (m-80) cc_final: 0.8372 (m-80) REVERT: F 3 LEU cc_start: 0.9374 (tp) cc_final: 0.9171 (tp) REVERT: F 4 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8462 (mm110) REVERT: F 23 MET cc_start: 0.9396 (mmm) cc_final: 0.8991 (mpp) REVERT: F 41 TYR cc_start: 0.9143 (m-80) cc_final: 0.8936 (m-80) REVERT: F 42 SER cc_start: 0.9223 (m) cc_final: 0.8626 (p) REVERT: G 58 ASN cc_start: 0.9512 (m-40) cc_final: 0.9141 (t0) REVERT: G 124 LEU cc_start: 0.8879 (mt) cc_final: 0.8530 (tp) REVERT: G 131 CYS cc_start: 0.7412 (t) cc_final: 0.7000 (t) REVERT: G 144 LYS cc_start: 0.9463 (tttm) cc_final: 0.9260 (tppt) REVERT: G 171 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8762 (mtt180) REVERT: G 182 GLN cc_start: 0.8234 (mt0) cc_final: 0.7810 (tt0) REVERT: G 204 MET cc_start: 0.8985 (tmm) cc_final: 0.8544 (tmm) REVERT: G 282 LEU cc_start: 0.9319 (mt) cc_final: 0.9092 (mp) REVERT: G 299 LEU cc_start: 0.9476 (tp) cc_final: 0.9032 (tp) REVERT: G 300 VAL cc_start: 0.9555 (t) cc_final: 0.9335 (t) REVERT: G 376 TYR cc_start: 0.8985 (m-80) cc_final: 0.8567 (m-80) REVERT: H 108 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9128 (tm-30) REVERT: H 114 ASP cc_start: 0.8559 (t0) cc_final: 0.8052 (m-30) REVERT: H 119 GLN cc_start: 0.9426 (mt0) cc_final: 0.9016 (tm-30) REVERT: H 123 PHE cc_start: 0.8968 (p90) cc_final: 0.8719 (p90) REVERT: H 144 PHE cc_start: 0.8635 (m-80) cc_final: 0.8104 (m-80) REVERT: J 49 LYS cc_start: 0.8202 (mttt) cc_final: 0.7674 (mmtm) REVERT: J 56 MET cc_start: 0.8207 (ttp) cc_final: 0.7910 (mtp) REVERT: K 235 MET cc_start: 0.6321 (ttt) cc_final: 0.5370 (tmm) REVERT: K 268 PHE cc_start: 0.9213 (m-80) cc_final: 0.8830 (m-80) REVERT: K 292 LEU cc_start: 0.9473 (tp) cc_final: 0.8844 (pp) REVERT: K 488 PRO cc_start: 0.2348 (Cg_exo) cc_final: 0.1551 (Cg_endo) REVERT: c 211 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7374 (mmm160) REVERT: c 216 PHE cc_start: 0.8434 (p90) cc_final: 0.8210 (p90) REVERT: c 260 MET cc_start: 0.9481 (ttp) cc_final: 0.9276 (ttm) REVERT: c 290 GLU cc_start: 0.9338 (mp0) cc_final: 0.9121 (mp0) REVERT: c 350 MET cc_start: 0.9050 (mtt) cc_final: 0.8754 (mtt) REVERT: d 78 HIS cc_start: 0.9002 (p-80) cc_final: 0.8754 (p90) REVERT: d 82 ASP cc_start: 0.9489 (m-30) cc_final: 0.9287 (t0) REVERT: d 87 LYS cc_start: 0.8643 (tttt) cc_final: 0.8318 (tptt) REVERT: d 113 VAL cc_start: 0.8847 (t) cc_final: 0.8568 (m) REVERT: d 120 LEU cc_start: 0.8879 (mp) cc_final: 0.8136 (pp) REVERT: d 125 PHE cc_start: 0.7696 (p90) cc_final: 0.7257 (p90) REVERT: e 59 GLN cc_start: 0.8221 (mm110) cc_final: 0.7753 (mt0) REVERT: e 78 ILE cc_start: 0.8803 (tt) cc_final: 0.8561 (tp) REVERT: e 79 MET cc_start: 0.9457 (ttm) cc_final: 0.9134 (mpp) REVERT: e 81 LEU cc_start: 0.9288 (mt) cc_final: 0.9048 (mp) REVERT: e 99 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9212 (mt-10) REVERT: e 105 TYR cc_start: 0.9506 (p90) cc_final: 0.8968 (p90) REVERT: e 113 ASP cc_start: 0.9238 (m-30) cc_final: 0.8821 (t0) REVERT: e 128 MET cc_start: 0.8655 (ttp) cc_final: 0.7787 (tpp) REVERT: e 141 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9408 (mt-10) REVERT: f 2 PHE cc_start: 0.8652 (m-80) cc_final: 0.8406 (m-80) REVERT: f 4 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8465 (mm110) REVERT: f 23 MET cc_start: 0.9395 (mmm) cc_final: 0.8990 (mpp) REVERT: f 42 SER cc_start: 0.9225 (m) cc_final: 0.8630 (p) REVERT: g 58 ASN cc_start: 0.9512 (m-40) cc_final: 0.9141 (t0) REVERT: g 124 LEU cc_start: 0.8881 (mt) cc_final: 0.8529 (tp) REVERT: g 131 CYS cc_start: 0.7504 (t) cc_final: 0.7099 (t) REVERT: g 144 LYS cc_start: 0.9467 (tttm) cc_final: 0.9263 (tppt) REVERT: g 171 ARG cc_start: 0.9106 (mtt180) cc_final: 0.8759 (mtt180) REVERT: g 204 MET cc_start: 0.8965 (tmm) cc_final: 0.8526 (tmm) REVERT: g 282 LEU cc_start: 0.9320 (mt) cc_final: 0.9091 (mp) REVERT: g 299 LEU cc_start: 0.9471 (tp) cc_final: 0.8974 (tp) REVERT: g 300 VAL cc_start: 0.9547 (t) cc_final: 0.9313 (t) REVERT: g 376 TYR cc_start: 0.8982 (m-80) cc_final: 0.8554 (m-80) REVERT: h 108 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9141 (tm-30) REVERT: h 114 ASP cc_start: 0.8558 (t0) cc_final: 0.8098 (m-30) REVERT: h 119 GLN cc_start: 0.9432 (mt0) cc_final: 0.9017 (tm-30) REVERT: h 123 PHE cc_start: 0.8976 (p90) cc_final: 0.8724 (p90) REVERT: h 144 PHE cc_start: 0.8628 (m-80) cc_final: 0.8099 (m-80) REVERT: j 49 LYS cc_start: 0.8196 (mttt) cc_final: 0.7670 (mmtm) REVERT: j 56 MET cc_start: 0.8203 (ttp) cc_final: 0.7914 (mtp) REVERT: k 235 MET cc_start: 0.6332 (ttt) cc_final: 0.5378 (tmm) REVERT: k 268 PHE cc_start: 0.9212 (m-80) cc_final: 0.8832 (m-80) REVERT: k 292 LEU cc_start: 0.9478 (tp) cc_final: 0.8872 (pp) REVERT: k 488 PRO cc_start: 0.2324 (Cg_exo) cc_final: 0.1564 (Cg_endo) outliers start: 8 outliers final: 2 residues processed: 768 average time/residue: 0.2451 time to fit residues: 288.9565 Evaluate side-chains 399 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain k residue 310 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 168 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 275 ASN D 155 GLN E 68 GLN G 160 HIS G 264 HIS I 68 GLN J 4 GLN J 31 HIS J 44 HIS K 167 GLN c 168 GLN c 244 GLN c 275 ASN d 155 GLN e 68 GLN g 160 HIS g 264 HIS i 68 GLN j 4 GLN j 31 HIS j 44 HIS k 167 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.075693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.055710 restraints weight = 220767.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.057239 restraints weight = 112105.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.058184 restraints weight = 74871.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.058769 restraints weight = 58998.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059048 restraints weight = 51421.013| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 36244 Z= 0.216 Angle : 0.721 16.935 50838 Z= 0.385 Chirality : 0.043 0.269 5938 Planarity : 0.005 0.076 5096 Dihedral : 19.732 109.385 9672 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.13 % Allowed : 10.69 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.96 (0.14), residues: 3296 helix: -0.11 (0.18), residues: 766 sheet: -1.85 (0.17), residues: 702 loop : -0.21 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 158 TYR 0.025 0.002 TYR E 107 PHE 0.025 0.002 PHE G 181 TRP 0.015 0.002 TRP g 380 HIS 0.007 0.002 HIS K 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (36244) covalent geometry : angle 0.72146 / 0.38 (50838) hydrogen bonds : bond 0.06558 / 4.55 ( 1173) hydrogen bonds : angle 5.66908 / 3.88 ( 2839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 414 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5755 (ttm170) REVERT: C 254 MET cc_start: 0.8480 (mmm) cc_final: 0.8113 (mmm) REVERT: D 87 LYS cc_start: 0.8513 (tttt) cc_final: 0.8178 (tptt) REVERT: D 120 LEU cc_start: 0.8951 (mp) cc_final: 0.8154 (pp) REVERT: E 113 ASP cc_start: 0.8847 (m-30) cc_final: 0.8634 (t0) REVERT: E 149 LEU cc_start: 0.8569 (mt) cc_final: 0.8356 (mt) REVERT: F 2 PHE cc_start: 0.7629 (m-80) cc_final: 0.7346 (m-80) REVERT: F 42 SER cc_start: 0.8737 (m) cc_final: 0.8286 (p) REVERT: G 124 LEU cc_start: 0.8572 (mt) cc_final: 0.8214 (tp) REVERT: G 204 MET cc_start: 0.8520 (tmm) cc_final: 0.7827 (tmm) REVERT: G 228 THR cc_start: 0.9088 (m) cc_final: 0.8659 (p) REVERT: G 316 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7808 (mmp) REVERT: G 317 LEU cc_start: 0.7378 (tt) cc_final: 0.7031 (tt) REVERT: H 119 GLN cc_start: 0.9136 (mt0) cc_final: 0.8865 (mm110) REVERT: H 121 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: H 123 PHE cc_start: 0.8300 (p90) cc_final: 0.8048 (p90) REVERT: H 125 PHE cc_start: 0.8001 (p90) cc_final: 0.7642 (p90) REVERT: H 157 PHE cc_start: 0.8428 (m-80) cc_final: 0.8132 (m-80) REVERT: J 55 LEU cc_start: 0.8191 (mt) cc_final: 0.7853 (mt) REVERT: K 235 MET cc_start: 0.4658 (ttt) cc_final: 0.4266 (tmm) REVERT: K 268 PHE cc_start: 0.7953 (m-80) cc_final: 0.6881 (m-80) REVERT: K 292 LEU cc_start: 0.9416 (tp) cc_final: 0.8815 (pp) REVERT: c 158 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5640 (ttm170) REVERT: c 254 MET cc_start: 0.8459 (mmm) cc_final: 0.8095 (mmm) REVERT: d 87 LYS cc_start: 0.8515 (tttt) cc_final: 0.8203 (tptt) REVERT: d 120 LEU cc_start: 0.8960 (mp) cc_final: 0.8169 (pp) REVERT: e 149 LEU cc_start: 0.8552 (mt) cc_final: 0.8341 (mt) REVERT: f 2 PHE cc_start: 0.7541 (m-80) cc_final: 0.7311 (m-80) REVERT: f 40 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8896 (pptt) REVERT: f 42 SER cc_start: 0.8731 (m) cc_final: 0.8285 (p) REVERT: g 124 LEU cc_start: 0.8603 (mt) cc_final: 0.8259 (tp) REVERT: g 204 MET cc_start: 0.8521 (tmm) cc_final: 0.7776 (tmm) REVERT: g 228 THR cc_start: 0.9059 (m) cc_final: 0.8550 (p) REVERT: g 316 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7816 (mmp) REVERT: g 317 LEU cc_start: 0.7379 (tt) cc_final: 0.7019 (tt) REVERT: h 119 GLN cc_start: 0.9140 (mt0) cc_final: 0.8853 (mm110) REVERT: h 121 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: h 123 PHE cc_start: 0.8294 (p90) cc_final: 0.8029 (p90) REVERT: h 125 PHE cc_start: 0.7964 (p90) cc_final: 0.7626 (p90) REVERT: h 157 PHE cc_start: 0.8426 (m-80) cc_final: 0.8131 (m-80) REVERT: j 55 LEU cc_start: 0.8224 (mt) cc_final: 0.7893 (mt) REVERT: k 197 ASN cc_start: 0.7529 (m-40) cc_final: 0.6902 (t0) REVERT: k 235 MET cc_start: 0.4697 (ttt) cc_final: 0.4293 (tmm) REVERT: k 268 PHE cc_start: 0.7942 (m-80) cc_final: 0.6869 (m-80) REVERT: k 292 LEU cc_start: 0.9430 (tp) cc_final: 0.8810 (pp) outliers start: 63 outliers final: 29 residues processed: 445 average time/residue: 0.2353 time to fit residues: 164.0231 Evaluate side-chains 357 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain c residue 142 LEU Chi-restraints excluded: chain c residue 158 ARG Chi-restraints excluded: chain c residue 182 GLN Chi-restraints excluded: chain c residue 239 VAL Chi-restraints excluded: chain c residue 244 GLN Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 218 VAL Chi-restraints excluded: chain g residue 316 MET Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain k residue 195 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 199 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 chunk 125 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 305 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN D 155 GLN G 146 GLN G 168 GLN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 HIS c 244 GLN d 155 GLN g 146 GLN g 168 GLN ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 366 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.072697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052608 restraints weight = 220262.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.054045 restraints weight = 114133.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.054906 restraints weight = 77220.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.055417 restraints weight = 61406.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.055731 restraints weight = 53934.875| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 36244 Z= 0.228 Angle : 0.688 18.616 50838 Z= 0.360 Chirality : 0.042 0.235 5938 Planarity : 0.006 0.077 5096 Dihedral : 19.867 107.700 9664 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 11.40 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.75 (0.14), residues: 3296 helix: -0.09 (0.18), residues: 774 sheet: -1.47 (0.17), residues: 728 loop : -0.10 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 171 TYR 0.021 0.002 TYR i 91 PHE 0.019 0.002 PHE f 20 TRP 0.011 0.001 TRP k 395 HIS 0.009 0.002 HIS g 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (36244) covalent geometry : angle 0.68800 / 0.36 (50838) hydrogen bonds : bond 0.05770 / 4.11 ( 1173) hydrogen bonds : angle 5.36745 / 3.70 ( 2839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 341 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6004 (ttm-80) REVERT: C 183 ARG cc_start: 0.6999 (ttt180) cc_final: 0.6725 (ttt180) REVERT: C 316 MET cc_start: 0.7860 (mtm) cc_final: 0.7631 (mpp) REVERT: C 350 MET cc_start: 0.7181 (mtt) cc_final: 0.6979 (mpp) REVERT: D 120 LEU cc_start: 0.8944 (mp) cc_final: 0.7589 (pt) REVERT: D 125 PHE cc_start: 0.8102 (p90) cc_final: 0.7160 (p90) REVERT: D 132 ASN cc_start: 0.8475 (p0) cc_final: 0.8189 (p0) REVERT: F 18 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8154 (mtmm) REVERT: F 42 SER cc_start: 0.8689 (m) cc_final: 0.8236 (p) REVERT: G 124 LEU cc_start: 0.8682 (mt) cc_final: 0.8442 (tp) REVERT: G 204 MET cc_start: 0.8224 (tmm) cc_final: 0.7925 (tmm) REVERT: G 243 MET cc_start: 0.9201 (tmm) cc_final: 0.8950 (tmm) REVERT: G 316 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7792 (mmp) REVERT: H 119 GLN cc_start: 0.9254 (mt0) cc_final: 0.9030 (mm110) REVERT: H 121 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7713 (mtt90) REVERT: H 123 PHE cc_start: 0.8454 (p90) cc_final: 0.7988 (p90) REVERT: H 125 PHE cc_start: 0.7985 (p90) cc_final: 0.7592 (p90) REVERT: I 114 LEU cc_start: 0.8605 (tp) cc_final: 0.8129 (tt) REVERT: J 55 LEU cc_start: 0.8400 (mt) cc_final: 0.8046 (mt) REVERT: K 197 ASN cc_start: 0.7322 (m-40) cc_final: 0.6644 (t0) REVERT: K 235 MET cc_start: 0.4779 (ttt) cc_final: 0.4169 (tmm) REVERT: K 268 PHE cc_start: 0.8059 (m-80) cc_final: 0.6999 (m-80) REVERT: K 292 LEU cc_start: 0.9417 (tp) cc_final: 0.8736 (pp) REVERT: c 158 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5925 (ttm-80) REVERT: c 316 MET cc_start: 0.7848 (mtm) cc_final: 0.7627 (mpp) REVERT: c 350 MET cc_start: 0.7196 (mtt) cc_final: 0.6979 (mpp) REVERT: d 120 LEU cc_start: 0.8937 (mp) cc_final: 0.7587 (pt) REVERT: d 125 PHE cc_start: 0.8115 (p90) cc_final: 0.7227 (p90) REVERT: d 132 ASN cc_start: 0.8472 (p0) cc_final: 0.8188 (p0) REVERT: f 18 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8144 (mtmm) REVERT: f 42 SER cc_start: 0.8805 (m) cc_final: 0.8334 (p) REVERT: g 124 LEU cc_start: 0.8679 (mt) cc_final: 0.8442 (tp) REVERT: g 204 MET cc_start: 0.8231 (tmm) cc_final: 0.7968 (tmm) REVERT: g 243 MET cc_start: 0.9206 (tmm) cc_final: 0.8961 (tmm) REVERT: g 316 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7795 (mmp) REVERT: h 119 GLN cc_start: 0.9259 (mt0) cc_final: 0.9032 (mm110) REVERT: h 121 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7699 (mtt90) REVERT: h 123 PHE cc_start: 0.8443 (p90) cc_final: 0.7971 (p90) REVERT: h 125 PHE cc_start: 0.7973 (p90) cc_final: 0.7583 (p90) REVERT: i 114 LEU cc_start: 0.8608 (tp) cc_final: 0.8130 (tt) REVERT: j 55 LEU cc_start: 0.8396 (mt) cc_final: 0.8096 (mt) REVERT: k 197 ASN cc_start: 0.7337 (m-40) cc_final: 0.6661 (t0) REVERT: k 235 MET cc_start: 0.4802 (ttt) cc_final: 0.4194 (tmm) REVERT: k 268 PHE cc_start: 0.8056 (m-80) cc_final: 0.6996 (m-80) REVERT: k 292 LEU cc_start: 0.9401 (tp) cc_final: 0.8717 (pp) outliers start: 85 outliers final: 48 residues processed: 395 average time/residue: 0.2204 time to fit residues: 138.0535 Evaluate side-chains 351 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 273 TYR Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 142 LEU Chi-restraints excluded: chain c residue 158 ARG Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 168 GLN Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 273 TYR Chi-restraints excluded: chain g residue 316 MET Chi-restraints excluded: chain g residue 323 TYR Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 159 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 GLN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS c 68 HIS d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 GLN ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 273 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.072050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052118 restraints weight = 218604.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.053506 restraints weight = 113807.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.054387 restraints weight = 77146.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.054919 restraints weight = 61082.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055181 restraints weight = 53374.914| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 36244 Z= 0.176 Angle : 0.627 16.894 50838 Z= 0.324 Chirality : 0.039 0.192 5938 Planarity : 0.005 0.072 5096 Dihedral : 19.848 105.124 9664 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.06 % Allowed : 13.43 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3296 helix: 0.04 (0.18), residues: 774 sheet: -1.47 (0.17), residues: 760 loop : -0.04 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 158 TYR 0.022 0.002 TYR h 103 PHE 0.021 0.002 PHE e 70 TRP 0.008 0.001 TRP K 395 HIS 0.008 0.001 HIS g 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (36244) covalent geometry : angle 0.62726 / 0.32 (50838) hydrogen bonds : bond 0.05055 / 3.59 ( 1173) hydrogen bonds : angle 5.14261 / 3.59 ( 2839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6459 (ttm-80) REVERT: C 183 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6949 (ttt180) REVERT: C 316 MET cc_start: 0.7760 (mtm) cc_final: 0.7498 (mpp) REVERT: D 78 HIS cc_start: 0.8229 (p90) cc_final: 0.8008 (p90) REVERT: F 42 SER cc_start: 0.8698 (m) cc_final: 0.8246 (p) REVERT: F 49 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8801 (mttm) REVERT: G 124 LEU cc_start: 0.8694 (mt) cc_final: 0.8468 (tp) REVERT: G 201 GLU cc_start: 0.8251 (mp0) cc_final: 0.7976 (pm20) REVERT: G 204 MET cc_start: 0.8276 (tmm) cc_final: 0.7793 (tmm) REVERT: G 243 MET cc_start: 0.9149 (tmm) cc_final: 0.8933 (tmm) REVERT: H 119 GLN cc_start: 0.9320 (mt0) cc_final: 0.9088 (mm110) REVERT: H 121 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7783 (mtt90) REVERT: H 123 PHE cc_start: 0.8456 (p90) cc_final: 0.8069 (p90) REVERT: H 125 PHE cc_start: 0.8016 (p90) cc_final: 0.7611 (p90) REVERT: I 114 LEU cc_start: 0.8662 (tp) cc_final: 0.8232 (tt) REVERT: J 55 LEU cc_start: 0.8328 (mt) cc_final: 0.8053 (mt) REVERT: K 197 ASN cc_start: 0.7451 (m-40) cc_final: 0.6504 (t0) REVERT: K 235 MET cc_start: 0.4946 (ttt) cc_final: 0.3949 (tmm) REVERT: K 268 PHE cc_start: 0.8118 (m-80) cc_final: 0.7076 (m-80) REVERT: K 292 LEU cc_start: 0.9359 (tp) cc_final: 0.8663 (pp) REVERT: c 316 MET cc_start: 0.7746 (mtm) cc_final: 0.7494 (mpp) REVERT: d 78 HIS cc_start: 0.8231 (p90) cc_final: 0.8011 (p90) REVERT: f 42 SER cc_start: 0.8812 (m) cc_final: 0.8324 (p) REVERT: f 49 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8796 (mttm) REVERT: g 124 LEU cc_start: 0.8696 (mt) cc_final: 0.8476 (tp) REVERT: g 201 GLU cc_start: 0.8212 (mp0) cc_final: 0.7979 (pm20) REVERT: g 243 MET cc_start: 0.9159 (tmm) cc_final: 0.8955 (tmm) REVERT: h 119 GLN cc_start: 0.9352 (mt0) cc_final: 0.9115 (mm110) REVERT: h 121 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7785 (mtt90) REVERT: h 123 PHE cc_start: 0.8455 (p90) cc_final: 0.8086 (p90) REVERT: h 125 PHE cc_start: 0.8000 (p90) cc_final: 0.7594 (p90) REVERT: i 114 LEU cc_start: 0.8663 (tp) cc_final: 0.8231 (tt) REVERT: j 55 LEU cc_start: 0.8326 (mt) cc_final: 0.8047 (mt) REVERT: k 197 ASN cc_start: 0.7460 (m-40) cc_final: 0.6516 (t0) REVERT: k 235 MET cc_start: 0.4914 (ttt) cc_final: 0.3921 (tmm) REVERT: k 268 PHE cc_start: 0.8109 (m-80) cc_final: 0.7060 (m-80) REVERT: k 292 LEU cc_start: 0.9383 (tp) cc_final: 0.8701 (pp) outliers start: 61 outliers final: 41 residues processed: 357 average time/residue: 0.2253 time to fit residues: 128.6478 Evaluate side-chains 332 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 220 MET Chi-restraints excluded: chain c residue 142 LEU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 168 GLN Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 220 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 310 optimal weight: 50.0000 chunk 207 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 164 optimal weight: 50.0000 chunk 266 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 GLN c 232 HIS d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.071566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051453 restraints weight = 222674.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052855 restraints weight = 116520.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.053691 restraints weight = 78808.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054202 restraints weight = 62950.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.054485 restraints weight = 55459.367| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 36244 Z= 0.179 Angle : 0.619 16.287 50838 Z= 0.320 Chirality : 0.039 0.201 5938 Planarity : 0.005 0.073 5096 Dihedral : 19.857 104.697 9664 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.57 % Allowed : 14.24 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.57 (0.15), residues: 3296 helix: 0.11 (0.19), residues: 776 sheet: -1.39 (0.18), residues: 750 loop : 0.03 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 158 TYR 0.020 0.002 TYR H 103 PHE 0.018 0.002 PHE H 144 TRP 0.009 0.001 TRP K 177 HIS 0.008 0.001 HIS K 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (36244) covalent geometry : angle 0.61911 / 0.32 (50838) hydrogen bonds : bond 0.04852 / 3.45 ( 1173) hydrogen bonds : angle 5.04229 / 3.53 ( 2839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 316 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.8473 (mmm) cc_final: 0.8100 (mmm) REVERT: F 42 SER cc_start: 0.8745 (m) cc_final: 0.8174 (p) REVERT: F 49 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8814 (mttm) REVERT: G 175 THR cc_start: 0.9388 (m) cc_final: 0.9118 (p) REVERT: G 201 GLU cc_start: 0.8304 (mp0) cc_final: 0.8088 (pm20) REVERT: G 316 MET cc_start: 0.7896 (mmp) cc_final: 0.7280 (mmp) REVERT: H 119 GLN cc_start: 0.9334 (mt0) cc_final: 0.9110 (tp40) REVERT: H 121 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7957 (mtt90) REVERT: H 123 PHE cc_start: 0.8420 (p90) cc_final: 0.8026 (p90) REVERT: H 125 PHE cc_start: 0.8054 (p90) cc_final: 0.7631 (p90) REVERT: I 114 LEU cc_start: 0.8677 (tp) cc_final: 0.8403 (tt) REVERT: J 55 LEU cc_start: 0.8378 (mt) cc_final: 0.8124 (mt) REVERT: K 197 ASN cc_start: 0.7359 (m-40) cc_final: 0.6821 (t0) REVERT: K 214 MET cc_start: 0.7237 (tpp) cc_final: 0.6948 (tpt) REVERT: K 235 MET cc_start: 0.5044 (ttt) cc_final: 0.4010 (tmm) REVERT: K 268 PHE cc_start: 0.8142 (m-80) cc_final: 0.7183 (m-80) REVERT: K 292 LEU cc_start: 0.9326 (tp) cc_final: 0.8686 (pp) REVERT: c 183 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7431 (ttt180) REVERT: f 42 SER cc_start: 0.8872 (m) cc_final: 0.8249 (p) REVERT: f 49 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8804 (mttm) REVERT: g 316 MET cc_start: 0.7936 (mmp) cc_final: 0.7334 (mmp) REVERT: h 119 GLN cc_start: 0.9337 (mt0) cc_final: 0.9103 (tp40) REVERT: h 121 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7950 (mtt90) REVERT: h 123 PHE cc_start: 0.8415 (p90) cc_final: 0.8022 (p90) REVERT: h 125 PHE cc_start: 0.8048 (p90) cc_final: 0.7625 (p90) REVERT: i 114 LEU cc_start: 0.8679 (tp) cc_final: 0.8402 (tt) REVERT: j 55 LEU cc_start: 0.8423 (mt) cc_final: 0.8148 (mt) REVERT: k 197 ASN cc_start: 0.7361 (m-40) cc_final: 0.6841 (t0) REVERT: k 214 MET cc_start: 0.7238 (tpp) cc_final: 0.6956 (tpt) REVERT: k 235 MET cc_start: 0.5189 (ttt) cc_final: 0.4208 (tmm) REVERT: k 268 PHE cc_start: 0.8135 (m-80) cc_final: 0.7186 (m-80) REVERT: k 292 LEU cc_start: 0.9338 (tp) cc_final: 0.8639 (pp) outliers start: 76 outliers final: 46 residues processed: 361 average time/residue: 0.2284 time to fit residues: 133.3487 Evaluate side-chains 314 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 220 MET Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 220 MET Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 131 optimal weight: 8.9990 chunk 355 optimal weight: 50.0000 chunk 354 optimal weight: 50.0000 chunk 101 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 303 optimal weight: 30.0000 chunk 205 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 GLN d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.071292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051195 restraints weight = 223825.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052531 restraints weight = 118462.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053371 restraints weight = 81422.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053875 restraints weight = 65105.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.054174 restraints weight = 57411.133| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 36244 Z= 0.163 Angle : 0.608 13.268 50838 Z= 0.313 Chirality : 0.039 0.163 5938 Planarity : 0.005 0.074 5096 Dihedral : 19.835 104.909 9664 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.60 % Allowed : 14.95 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.47 (0.15), residues: 3296 helix: 0.22 (0.19), residues: 778 sheet: -1.34 (0.18), residues: 738 loop : 0.09 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 114 TYR 0.018 0.002 TYR H 103 PHE 0.022 0.002 PHE D 125 TRP 0.008 0.001 TRP K 231 HIS 0.008 0.001 HIS K 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (36244) covalent geometry : angle 0.60780 / 0.31 (50838) hydrogen bonds : bond 0.04545 / 3.23 ( 1173) hydrogen bonds : angle 4.98337 / 3.50 ( 2839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 302 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 350 MET cc_start: 0.7398 (mtt) cc_final: 0.7112 (mpp) REVERT: D 141 LEU cc_start: 0.9067 (tp) cc_final: 0.8832 (mm) REVERT: E 62 ARG cc_start: 0.7844 (mmm160) cc_final: 0.6957 (mmm160) REVERT: E 98 CYS cc_start: 0.9183 (m) cc_final: 0.8801 (m) REVERT: F 42 SER cc_start: 0.8666 (m) cc_final: 0.8070 (p) REVERT: F 49 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8776 (mttm) REVERT: G 171 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7214 (tpp80) REVERT: G 175 THR cc_start: 0.9354 (m) cc_final: 0.8685 (p) REVERT: G 316 MET cc_start: 0.8048 (mmp) cc_final: 0.7378 (mmp) REVERT: G 371 MET cc_start: 0.7854 (tmm) cc_final: 0.7586 (tmm) REVERT: H 121 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7832 (mtt90) REVERT: H 123 PHE cc_start: 0.8396 (p90) cc_final: 0.8114 (p90) REVERT: H 125 PHE cc_start: 0.8034 (p90) cc_final: 0.7682 (p90) REVERT: I 114 LEU cc_start: 0.8704 (tp) cc_final: 0.8441 (tt) REVERT: J 55 LEU cc_start: 0.8477 (mt) cc_final: 0.8210 (mt) REVERT: K 197 ASN cc_start: 0.7464 (m-40) cc_final: 0.6846 (t0) REVERT: K 235 MET cc_start: 0.5006 (ttt) cc_final: 0.3942 (tmm) REVERT: K 268 PHE cc_start: 0.8162 (m-80) cc_final: 0.7207 (m-80) REVERT: K 292 LEU cc_start: 0.9319 (tp) cc_final: 0.8668 (pp) REVERT: c 254 MET cc_start: 0.8432 (mmm) cc_final: 0.8102 (mmm) REVERT: c 350 MET cc_start: 0.7402 (mtt) cc_final: 0.7111 (mpp) REVERT: e 62 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7017 (mmm160) REVERT: f 42 SER cc_start: 0.8797 (m) cc_final: 0.8176 (p) REVERT: g 175 THR cc_start: 0.9337 (m) cc_final: 0.8680 (p) REVERT: g 316 MET cc_start: 0.8027 (mmp) cc_final: 0.7341 (mmp) REVERT: g 371 MET cc_start: 0.7822 (tmm) cc_final: 0.7554 (tmm) REVERT: h 121 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7854 (mtt90) REVERT: h 123 PHE cc_start: 0.8365 (p90) cc_final: 0.8104 (p90) REVERT: h 125 PHE cc_start: 0.8017 (p90) cc_final: 0.7637 (p90) REVERT: h 133 MET cc_start: 0.7413 (tpp) cc_final: 0.7027 (tpp) REVERT: i 114 LEU cc_start: 0.8690 (tp) cc_final: 0.8429 (tt) REVERT: j 55 LEU cc_start: 0.8470 (mt) cc_final: 0.8197 (mt) REVERT: k 197 ASN cc_start: 0.7476 (m-40) cc_final: 0.6862 (t0) REVERT: k 235 MET cc_start: 0.5086 (ttt) cc_final: 0.4070 (tmm) REVERT: k 268 PHE cc_start: 0.8147 (m-80) cc_final: 0.7203 (m-80) REVERT: k 292 LEU cc_start: 0.9313 (tp) cc_final: 0.8651 (pp) outliers start: 77 outliers final: 50 residues processed: 350 average time/residue: 0.2181 time to fit residues: 123.0525 Evaluate side-chains 320 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain d residue 124 TYR Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 218 VAL Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 127 ILE Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 26 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 chunk 337 optimal weight: 50.0000 chunk 318 optimal weight: 50.0000 chunk 137 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN ** g 99 ASN ** 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 = 0.3861 r_free = 0.3861 target = 0.070334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050400 restraints weight = 225913.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.051748 restraints weight = 119861.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.052563 restraints weight = 81771.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052993 restraints weight = 65673.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053331 restraints weight = 58595.420| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 36244 Z= 0.202 Angle : 0.628 14.500 50838 Z= 0.324 Chirality : 0.040 0.219 5938 Planarity : 0.005 0.103 5096 Dihedral : 19.869 106.187 9664 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.71 % Allowed : 15.56 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.52 (0.15), residues: 3296 helix: 0.22 (0.19), residues: 776 sheet: -1.39 (0.18), residues: 734 loop : 0.03 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG e 61 TYR 0.018 0.002 TYR H 103 PHE 0.032 0.002 PHE E 70 TRP 0.008 0.001 TRP K 177 HIS 0.008 0.001 HIS k 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (36244) covalent geometry : angle 0.62810 / 0.32 (50838) hydrogen bonds : bond 0.05034 / 3.54 ( 1173) hydrogen bonds : angle 5.00677 / 3.51 ( 2839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 HIS cc_start: 0.8329 (p90) cc_final: 0.8057 (p90) REVERT: D 83 ASP cc_start: 0.8202 (m-30) cc_final: 0.7872 (t70) REVERT: E 98 CYS cc_start: 0.9142 (m) cc_final: 0.8660 (m) REVERT: E 105 TYR cc_start: 0.8950 (p90) cc_final: 0.8427 (p90) REVERT: E 144 GLU cc_start: 0.8540 (pp20) cc_final: 0.8105 (pp20) REVERT: F 40 LYS cc_start: 0.9316 (pptt) cc_final: 0.9005 (ptpp) REVERT: F 42 SER cc_start: 0.8766 (m) cc_final: 0.8208 (p) REVERT: G 316 MET cc_start: 0.8047 (mmp) cc_final: 0.7488 (mmp) REVERT: G 371 MET cc_start: 0.7912 (tmm) cc_final: 0.7694 (tmm) REVERT: H 116 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7822 (tp) REVERT: H 119 GLN cc_start: 0.8325 (tp40) cc_final: 0.8095 (tp40) REVERT: H 121 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7884 (mtt90) REVERT: H 133 MET cc_start: 0.7343 (tpp) cc_final: 0.7115 (tpp) REVERT: I 36 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: I 127 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8708 (mt) REVERT: J 55 LEU cc_start: 0.8521 (mt) cc_final: 0.8255 (mt) REVERT: K 197 ASN cc_start: 0.7338 (m-40) cc_final: 0.6568 (t0) REVERT: K 235 MET cc_start: 0.5192 (ttt) cc_final: 0.4272 (tmm) REVERT: K 268 PHE cc_start: 0.8146 (m-80) cc_final: 0.7237 (m-80) REVERT: K 292 LEU cc_start: 0.9307 (tp) cc_final: 0.8639 (pp) REVERT: c 243 MET cc_start: 0.7589 (mmm) cc_final: 0.7091 (tpt) REVERT: d 78 HIS cc_start: 0.8323 (p90) cc_final: 0.8064 (p90) REVERT: d 83 ASP cc_start: 0.8133 (m-30) cc_final: 0.7900 (t70) REVERT: e 98 CYS cc_start: 0.9053 (m) cc_final: 0.8699 (m) REVERT: e 128 MET cc_start: 0.8227 (tpp) cc_final: 0.7705 (tpp) REVERT: f 42 SER cc_start: 0.8816 (m) cc_final: 0.8253 (p) REVERT: g 316 MET cc_start: 0.8060 (mmp) cc_final: 0.7425 (mmt) REVERT: g 371 MET cc_start: 0.7909 (tmm) cc_final: 0.7694 (tmm) REVERT: h 116 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7808 (tp) REVERT: h 121 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7854 (mtt90) REVERT: i 36 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: j 55 LEU cc_start: 0.8514 (mt) cc_final: 0.8242 (mt) REVERT: k 197 ASN cc_start: 0.7500 (m-40) cc_final: 0.6748 (t0) REVERT: k 235 MET cc_start: 0.5251 (ttt) cc_final: 0.4283 (tmm) REVERT: k 268 PHE cc_start: 0.8138 (m-80) cc_final: 0.7226 (m-80) REVERT: k 292 LEU cc_start: 0.9319 (tp) cc_final: 0.8652 (pp) outliers start: 80 outliers final: 51 residues processed: 345 average time/residue: 0.2269 time to fit residues: 127.3589 Evaluate side-chains 318 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 343 ILE Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain d residue 91 ASP Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 218 VAL Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 121 optimal weight: 0.6980 chunk 303 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 283 optimal weight: 0.5980 chunk 320 optimal weight: 30.0000 chunk 343 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 333 optimal weight: 50.0000 chunk 338 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.071145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051301 restraints weight = 225149.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052653 restraints weight = 118262.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.053487 restraints weight = 80802.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054010 restraints weight = 64526.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054269 restraints weight = 56744.987| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36244 Z= 0.126 Angle : 0.582 13.549 50838 Z= 0.302 Chirality : 0.038 0.230 5938 Planarity : 0.005 0.109 5096 Dihedral : 19.813 106.154 9664 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.59 % Allowed : 16.98 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.42 (0.15), residues: 3296 helix: 0.30 (0.19), residues: 780 sheet: -1.33 (0.18), residues: 748 loop : 0.12 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 114 TYR 0.018 0.002 TYR I 91 PHE 0.021 0.002 PHE D 125 TRP 0.022 0.001 TRP g 217 HIS 0.010 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (36244) covalent geometry : angle 0.58230 / 0.30 (50838) hydrogen bonds : bond 0.04126 / 2.90 ( 1173) hydrogen bonds : angle 4.79232 / 3.37 ( 2839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 MET cc_start: 0.7591 (mmm) cc_final: 0.7288 (tpt) REVERT: D 78 HIS cc_start: 0.8292 (p90) cc_final: 0.8002 (p90) REVERT: D 83 ASP cc_start: 0.8060 (m-30) cc_final: 0.7646 (t70) REVERT: E 98 CYS cc_start: 0.9056 (m) cc_final: 0.8844 (m) REVERT: F 40 LYS cc_start: 0.9258 (pptt) cc_final: 0.8961 (ptpp) REVERT: F 42 SER cc_start: 0.8656 (m) cc_final: 0.8057 (p) REVERT: F 49 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8811 (mttm) REVERT: G 171 ARG cc_start: 0.8328 (mmp80) cc_final: 0.7973 (mtt180) REVERT: G 204 MET cc_start: 0.8918 (mmm) cc_final: 0.8640 (mmm) REVERT: G 243 MET cc_start: 0.8960 (tmm) cc_final: 0.8689 (tmm) REVERT: G 316 MET cc_start: 0.7998 (mmp) cc_final: 0.7399 (mmp) REVERT: G 371 MET cc_start: 0.7898 (tmm) cc_final: 0.7693 (tmm) REVERT: H 119 GLN cc_start: 0.8298 (tp40) cc_final: 0.8079 (tp40) REVERT: H 121 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7879 (mtt90) REVERT: H 125 PHE cc_start: 0.7885 (p90) cc_final: 0.7440 (p90) REVERT: J 55 LEU cc_start: 0.8557 (mt) cc_final: 0.8331 (mt) REVERT: K 197 ASN cc_start: 0.7371 (m-40) cc_final: 0.6531 (t0) REVERT: K 235 MET cc_start: 0.5155 (ttt) cc_final: 0.4214 (tmm) REVERT: K 268 PHE cc_start: 0.8115 (m-80) cc_final: 0.7161 (m-80) REVERT: K 292 LEU cc_start: 0.9307 (tp) cc_final: 0.8659 (pp) REVERT: c 183 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7791 (ttt180) REVERT: d 78 HIS cc_start: 0.8303 (p90) cc_final: 0.8013 (p90) REVERT: d 83 ASP cc_start: 0.8117 (m-30) cc_final: 0.7795 (t70) REVERT: e 128 MET cc_start: 0.8227 (tpp) cc_final: 0.7816 (tpp) REVERT: f 42 SER cc_start: 0.8724 (m) cc_final: 0.8091 (p) REVERT: g 316 MET cc_start: 0.7973 (mmp) cc_final: 0.7484 (mmp) REVERT: g 371 MET cc_start: 0.7944 (tmm) cc_final: 0.7743 (tmm) REVERT: h 125 PHE cc_start: 0.7941 (p90) cc_final: 0.7507 (p90) REVERT: j 55 LEU cc_start: 0.8558 (mt) cc_final: 0.8325 (mt) REVERT: k 176 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8296 (pttp) REVERT: k 197 ASN cc_start: 0.7532 (m-40) cc_final: 0.6725 (t0) REVERT: k 235 MET cc_start: 0.5196 (ttt) cc_final: 0.4235 (tmm) REVERT: k 268 PHE cc_start: 0.8103 (m-80) cc_final: 0.7148 (m-80) REVERT: k 292 LEU cc_start: 0.9305 (tp) cc_final: 0.8651 (pp) outliers start: 47 outliers final: 42 residues processed: 319 average time/residue: 0.2203 time to fit residues: 114.5348 Evaluate side-chains 314 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 270 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain e residue 100 ASP Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 218 VAL Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 176 LYS Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 302 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 355 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 chunk 336 optimal weight: 50.0000 chunk 175 optimal weight: 0.6980 chunk 363 optimal weight: 40.0000 chunk 342 optimal weight: 50.0000 chunk 123 optimal weight: 10.0000 chunk 153 optimal weight: 50.0000 overall best weight: 6.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 HIS ** g 99 ASN ** 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 = 0.3834 r_free = 0.3834 target = 0.069100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049216 restraints weight = 227437.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050532 restraints weight = 121236.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051334 restraints weight = 83329.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051826 restraints weight = 66927.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052021 restraints weight = 59059.651| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 36244 Z= 0.256 Angle : 0.700 14.585 50838 Z= 0.357 Chirality : 0.041 0.225 5938 Planarity : 0.006 0.104 5096 Dihedral : 19.934 108.973 9664 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.79 % Allowed : 17.05 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 3296 helix: 0.04 (0.19), residues: 780 sheet: -1.48 (0.18), residues: 754 loop : -0.04 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 62 TYR 0.021 0.002 TYR c 200 PHE 0.029 0.002 PHE e 70 TRP 0.010 0.002 TRP K 177 HIS 0.013 0.002 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 (36244) covalent geometry : angle 0.69977 / 0.36 (50838) hydrogen bonds : bond 0.05949 / 4.15 ( 1173) hydrogen bonds : angle 5.16484 / 3.63 ( 2839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 316 MET cc_start: 0.7816 (mpp) cc_final: 0.7431 (mpp) REVERT: C 345 MET cc_start: 0.8161 (tpp) cc_final: 0.7960 (tpp) REVERT: E 128 MET cc_start: 0.7998 (tpt) cc_final: 0.7687 (tpt) REVERT: F 42 SER cc_start: 0.8798 (m) cc_final: 0.8354 (p) REVERT: G 316 MET cc_start: 0.8056 (mmp) cc_final: 0.7660 (mmt) REVERT: H 121 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7944 (mtt90) REVERT: H 133 MET cc_start: 0.7320 (tpp) cc_final: 0.7107 (tpp) REVERT: I 36 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: J 55 LEU cc_start: 0.8612 (mt) cc_final: 0.8363 (mt) REVERT: K 197 ASN cc_start: 0.7482 (m-40) cc_final: 0.6630 (t0) REVERT: K 235 MET cc_start: 0.5425 (ttt) cc_final: 0.4536 (tmm) REVERT: K 268 PHE cc_start: 0.8117 (m-80) cc_final: 0.7211 (m-80) REVERT: K 292 LEU cc_start: 0.9317 (tp) cc_final: 0.8646 (pp) REVERT: K 320 LYS cc_start: 0.8950 (mttm) cc_final: 0.8710 (ptpp) REVERT: c 183 ARG cc_start: 0.8340 (ttt180) cc_final: 0.8098 (ttt90) REVERT: c 263 MET cc_start: 0.8270 (tpp) cc_final: 0.8057 (tpp) REVERT: c 316 MET cc_start: 0.7818 (mpp) cc_final: 0.7442 (mpp) REVERT: e 128 MET cc_start: 0.8227 (tpp) cc_final: 0.7805 (tpp) REVERT: f 42 SER cc_start: 0.8830 (m) cc_final: 0.8314 (p) REVERT: g 316 MET cc_start: 0.8065 (mmp) cc_final: 0.7679 (mmt) REVERT: h 119 GLN cc_start: 0.8441 (tp40) cc_final: 0.7551 (tm-30) REVERT: h 121 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: h 133 MET cc_start: 0.7101 (tpp) cc_final: 0.6442 (mtp) REVERT: i 36 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: j 55 LEU cc_start: 0.8622 (mt) cc_final: 0.8366 (mt) REVERT: k 197 ASN cc_start: 0.7422 (m-40) cc_final: 0.6580 (t0) REVERT: k 235 MET cc_start: 0.5588 (ttt) cc_final: 0.4922 (tmm) REVERT: k 268 PHE cc_start: 0.8098 (m-80) cc_final: 0.7201 (m-80) REVERT: k 292 LEU cc_start: 0.9313 (tp) cc_final: 0.8639 (pp) REVERT: k 320 LYS cc_start: 0.8921 (mttm) cc_final: 0.8688 (ptpp) outliers start: 53 outliers final: 43 residues processed: 302 average time/residue: 0.2254 time to fit residues: 110.5724 Evaluate side-chains 301 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 100 ASP Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain h residue 121 ARG Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 282 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 329 optimal weight: 50.0000 chunk 12 optimal weight: 0.0470 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 351 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 335 optimal weight: 40.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.069713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.049869 restraints weight = 226620.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051201 restraints weight = 119639.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052017 restraints weight = 81985.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052524 restraints weight = 65712.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052805 restraints weight = 57901.600| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 36244 Z= 0.169 Angle : 0.631 14.009 50838 Z= 0.325 Chirality : 0.040 0.212 5938 Planarity : 0.005 0.106 5096 Dihedral : 19.918 110.303 9664 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.76 % Allowed : 17.66 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3296 helix: 0.12 (0.19), residues: 790 sheet: -1.47 (0.18), residues: 760 loop : -0.02 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 114 TYR 0.019 0.002 TYR e 139 PHE 0.027 0.002 PHE d 125 TRP 0.023 0.001 TRP k 257 HIS 0.010 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (36244) covalent geometry : angle 0.63082 / 0.33 (50838) hydrogen bonds : bond 0.04696 / 3.31 ( 1173) hydrogen bonds : angle 4.98824 / 3.51 ( 2839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.8285 (mmm) cc_final: 0.8054 (mmm) REVERT: D 123 PHE cc_start: 0.6426 (p90) cc_final: 0.5966 (p90) REVERT: E 42 ARG cc_start: 0.8797 (tpp-160) cc_final: 0.8577 (tpp80) REVERT: F 40 LYS cc_start: 0.9293 (pptt) cc_final: 0.9087 (ptpp) REVERT: F 42 SER cc_start: 0.8797 (m) cc_final: 0.8185 (p) REVERT: F 49 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8964 (mtmm) REVERT: G 201 GLU cc_start: 0.8417 (pm20) cc_final: 0.7892 (pm20) REVERT: G 260 MET cc_start: 0.8307 (tpp) cc_final: 0.7991 (tpp) REVERT: G 316 MET cc_start: 0.8049 (mmp) cc_final: 0.7580 (mmp) REVERT: H 119 GLN cc_start: 0.8286 (tp40) cc_final: 0.7600 (tm-30) REVERT: H 133 MET cc_start: 0.7113 (tpp) cc_final: 0.6887 (tpp) REVERT: I 36 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: J 55 LEU cc_start: 0.8604 (mt) cc_final: 0.8369 (mt) REVERT: K 197 ASN cc_start: 0.7388 (m-40) cc_final: 0.6569 (t0) REVERT: K 235 MET cc_start: 0.5501 (ttt) cc_final: 0.4593 (tmm) REVERT: K 268 PHE cc_start: 0.8076 (m-80) cc_final: 0.7146 (m-80) REVERT: K 292 LEU cc_start: 0.9315 (tp) cc_final: 0.8643 (pp) REVERT: K 320 LYS cc_start: 0.8983 (mttm) cc_final: 0.8745 (ptpp) REVERT: c 183 ARG cc_start: 0.8314 (ttt180) cc_final: 0.7770 (ttm-80) REVERT: c 243 MET cc_start: 0.7747 (mmm) cc_final: 0.7168 (tpt) REVERT: d 123 PHE cc_start: 0.6453 (p90) cc_final: 0.6017 (p90) REVERT: e 42 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8348 (tpp-160) REVERT: e 105 TYR cc_start: 0.8920 (p90) cc_final: 0.8486 (p90) REVERT: e 128 MET cc_start: 0.8180 (tpp) cc_final: 0.7737 (tpp) REVERT: f 42 SER cc_start: 0.8807 (m) cc_final: 0.8225 (p) REVERT: f 49 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8887 (mtmm) REVERT: g 204 MET cc_start: 0.8589 (tpt) cc_final: 0.8352 (tpt) REVERT: g 316 MET cc_start: 0.8049 (mmp) cc_final: 0.7590 (mmp) REVERT: h 119 GLN cc_start: 0.8400 (tp40) cc_final: 0.7677 (tm-30) REVERT: h 133 MET cc_start: 0.7027 (tpp) cc_final: 0.6480 (mtp) REVERT: i 36 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: j 49 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7505 (mptt) REVERT: j 55 LEU cc_start: 0.8607 (mt) cc_final: 0.8364 (mt) REVERT: k 197 ASN cc_start: 0.7396 (m-40) cc_final: 0.6604 (t0) REVERT: k 235 MET cc_start: 0.5553 (ttt) cc_final: 0.4648 (tmm) REVERT: k 268 PHE cc_start: 0.8055 (m-80) cc_final: 0.7133 (m-80) REVERT: k 292 LEU cc_start: 0.9312 (tp) cc_final: 0.8636 (pp) REVERT: k 320 LYS cc_start: 0.8978 (mttm) cc_final: 0.8736 (ptpp) outliers start: 52 outliers final: 43 residues processed: 307 average time/residue: 0.2277 time to fit residues: 114.0459 Evaluate side-chains 305 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 260 PHE Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 100 ASP Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 176 LEU Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 363 VAL Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 92 GLU Chi-restraints excluded: chain h residue 103 TYR Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 65 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 350 optimal weight: 40.0000 chunk 329 optimal weight: 60.0000 chunk 200 optimal weight: 6.9990 chunk 278 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.069550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.049726 restraints weight = 226800.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.051048 restraints weight = 119991.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051878 restraints weight = 82598.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.052367 restraints weight = 66111.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052592 restraints weight = 58337.759| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 36244 Z= 0.168 Angle : 0.630 13.590 50838 Z= 0.323 Chirality : 0.039 0.205 5938 Planarity : 0.005 0.096 5096 Dihedral : 19.926 111.996 9664 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.73 % Allowed : 17.96 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.60 (0.15), residues: 3296 helix: 0.18 (0.19), residues: 788 sheet: -1.40 (0.18), residues: 760 loop : -0.03 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 114 TYR 0.018 0.002 TYR e 139 PHE 0.024 0.002 PHE h 123 TRP 0.012 0.001 TRP k 257 HIS 0.010 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (36244) covalent geometry : angle 0.63024 / 0.32 (50838) hydrogen bonds : bond 0.04659 / 3.26 ( 1173) hydrogen bonds : angle 4.97026 / 3.51 ( 2839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7007.93 seconds wall clock time: 121 minutes 54.41 seconds (7314.41 seconds total)