Starting phenix.real_space_refine on Tue Aug 26 09:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_52984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_52984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_52984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_52984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb3_52984/08_2025/9qb3_52984.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.93, per 1000 atoms: 0.20 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 4.30 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: 6.21 Time building geometry restraints manager: 3.53 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=" 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 bond pdb=" CG HIS c 68 " pdb=" CD2 HIS c 68 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.55e+00 ... (remaining 36239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 48414 2.66 - 5.31: 2362 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=" O3' G B 339 " pdb=" C3' G B 339 " pdb=" C2' G B 339 " ideal model delta sigma weight residual 113.70 106.32 7.38 1.50e+00 4.44e-01 2.42e+01 angle pdb=" O3' G b 339 " pdb=" C3' G b 339 " pdb=" C2' G b 339 " ideal model delta sigma weight residual 113.70 106.34 7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" O2' G b 345 " pdb=" C2' G b 345 " pdb=" C1' G b 345 " ideal model delta sigma weight residual 108.40 101.16 7.24 1.50e+00 4.44e-01 2.33e+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: 5091 0.127 - 0.254: 825 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: 0.01 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: 1.840 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 30.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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= 0.556 Angle : 1.242 13.283 50838 Z= 0.809 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 aren 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 covalent geometry : bond 0.00881 (36244) covalent geometry : angle 1.24217 (50838) hydrogen bonds : bond 0.21725 ( 1173) hydrogen bonds : angle 7.81080 ( 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 : 0.954 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: 0.1550 (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: 0.8804 (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: 0.2295 time to fit residues: 269.1198 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 : 1.158 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 168 GLN C 244 GLN C 275 ASN D 155 GLN G 146 GLN G 168 GLN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 HIS G 270 GLN I 68 GLN J 31 HIS J 44 HIS K 167 GLN c 68 HIS c 168 GLN c 244 GLN c 275 ASN d 155 GLN e 68 GLN g 146 GLN g 168 GLN ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 264 HIS g 270 GLN i 68 GLN j 31 HIS j 44 HIS k 167 GLN k 273 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.073412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.053443 restraints weight = 223519.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054886 restraints weight = 114282.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.055815 restraints weight = 76993.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.056358 restraints weight = 60696.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056665 restraints weight = 53260.906| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 36244 Z= 0.208 Angle : 0.713 17.114 50838 Z= 0.357 Chirality : 0.042 0.190 5938 Planarity : 0.005 0.058 5096 Dihedral : 19.885 110.964 9672 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.03 % Allowed : 10.62 % Favored : 87.35 % 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 aren not related in a simple way. whole: -0.71 (0.14), residues: 3296 helix: 0.05 (0.18), residues: 778 sheet: -1.80 (0.17), residues: 706 loop : 0.03 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 158 TYR 0.022 0.002 TYR i 91 PHE 0.016 0.002 PHE g 216 TRP 0.014 0.002 TRP C 108 HIS 0.007 0.001 HIS g 160 Details of bonding type rmsd covalent geometry : bond 0.00472 (36244) covalent geometry : angle 0.71264 (50838) hydrogen bonds : bond 0.05304 ( 1173) hydrogen bonds : angle 5.20085 ( 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 456 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 396 time to evaluate : 1.007 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 158 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6218 (ttm-80) REVERT: C 183 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6863 (ttt180) REVERT: C 316 MET cc_start: 0.7700 (mtm) cc_final: 0.7470 (mpp) REVERT: D 120 LEU cc_start: 0.8938 (mp) cc_final: 0.7569 (pt) REVERT: D 132 ASN cc_start: 0.8790 (p0) cc_final: 0.8584 (p0) REVERT: E 78 ILE cc_start: 0.9008 (tt) cc_final: 0.8537 (tp) REVERT: F 42 SER cc_start: 0.8550 (m) cc_final: 0.8099 (p) REVERT: F 49 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8793 (mttm) REVERT: G 124 LEU cc_start: 0.8601 (mt) cc_final: 0.8348 (tp) REVERT: G 181 PHE cc_start: 0.8721 (m-80) cc_final: 0.8452 (m-80) REVERT: G 204 MET cc_start: 0.8496 (tmm) cc_final: 0.7782 (tmm) REVERT: H 119 GLN cc_start: 0.9216 (mt0) cc_final: 0.9005 (mm110) REVERT: H 121 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: H 123 PHE cc_start: 0.8132 (p90) cc_final: 0.7789 (p90) REVERT: H 125 PHE cc_start: 0.8038 (p90) cc_final: 0.7785 (p90) REVERT: H 139 LYS cc_start: 0.9640 (mttm) cc_final: 0.9420 (tptt) REVERT: I 128 MET cc_start: 0.8884 (tmm) cc_final: 0.8240 (tmm) REVERT: J 55 LEU cc_start: 0.8259 (mt) cc_final: 0.7961 (mt) REVERT: K 197 ASN cc_start: 0.7494 (m-40) cc_final: 0.6883 (t0) REVERT: K 235 MET cc_start: 0.4726 (ttt) cc_final: 0.4109 (tmm) REVERT: K 268 PHE cc_start: 0.8064 (m-80) cc_final: 0.7078 (m-80) REVERT: K 292 LEU cc_start: 0.9368 (tp) cc_final: 0.8676 (pp) REVERT: c 183 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6889 (ttt180) REVERT: c 290 GLU cc_start: 0.8279 (mp0) cc_final: 0.7978 (mp0) REVERT: c 316 MET cc_start: 0.7686 (mtm) cc_final: 0.7462 (mpp) REVERT: d 120 LEU cc_start: 0.8869 (mp) cc_final: 0.7455 (pt) REVERT: e 78 ILE cc_start: 0.9007 (tt) cc_final: 0.8526 (tp) REVERT: e 105 TYR cc_start: 0.8963 (p90) cc_final: 0.8734 (p90) REVERT: f 42 SER cc_start: 0.8521 (m) cc_final: 0.8060 (p) REVERT: f 49 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8775 (mttm) REVERT: g 124 LEU cc_start: 0.8595 (mt) cc_final: 0.8340 (tp) REVERT: g 181 PHE cc_start: 0.8696 (m-80) cc_final: 0.8427 (m-80) REVERT: g 204 MET cc_start: 0.8509 (tmm) cc_final: 0.7782 (tmm) REVERT: h 119 GLN cc_start: 0.9207 (mt0) cc_final: 0.8988 (mm110) REVERT: h 121 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7671 (mtt90) REVERT: h 123 PHE cc_start: 0.8184 (p90) cc_final: 0.7850 (p90) REVERT: h 125 PHE cc_start: 0.8033 (p90) cc_final: 0.7783 (p90) REVERT: h 139 LYS cc_start: 0.9640 (mttm) cc_final: 0.9414 (tptt) REVERT: i 128 MET cc_start: 0.8887 (tmm) cc_final: 0.8244 (tmm) REVERT: j 55 LEU cc_start: 0.8250 (mt) cc_final: 0.7950 (mt) REVERT: k 197 ASN cc_start: 0.7509 (m-40) cc_final: 0.6905 (t0) REVERT: k 235 MET cc_start: 0.4767 (ttt) cc_final: 0.4145 (tmm) REVERT: k 268 PHE cc_start: 0.8017 (m-80) cc_final: 0.7021 (m-80) REVERT: k 292 LEU cc_start: 0.9372 (tp) cc_final: 0.8680 (pp) outliers start: 60 outliers final: 38 residues processed: 435 average time/residue: 0.2172 time to fit residues: 147.6982 Evaluate side-chains 337 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 296 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain F residue 21 ASP 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 199 ILE Chi-restraints excluded: chain G residue 218 VAL 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 H residue 136 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 244 GLN Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain c residue 335 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain f residue 21 ASP 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 199 ILE Chi-restraints excluded: chain g residue 218 VAL 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 h residue 136 SER Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 60 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 199 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 305 optimal weight: 50.0000 chunk 85 optimal weight: 9.9990 chunk 187 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 102 ASN G 160 HIS ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS K 366 HIS c 232 HIS d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN g 160 HIS ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 366 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.071431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051509 restraints weight = 221929.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052886 restraints weight = 115988.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053750 restraints weight = 78666.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.054256 restraints weight = 62541.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054492 restraints weight = 55083.458| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 36244 Z= 0.177 Angle : 0.640 13.872 50838 Z= 0.322 Chirality : 0.039 0.197 5938 Planarity : 0.005 0.063 5096 Dihedral : 19.881 102.503 9664 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 11.50 % Favored : 85.89 % 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 aren not related in a simple way. whole: -0.56 (0.14), residues: 3296 helix: 0.18 (0.18), residues: 784 sheet: -1.48 (0.18), residues: 696 loop : 0.01 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 158 TYR 0.020 0.002 TYR h 103 PHE 0.013 0.002 PHE j 2 TRP 0.016 0.001 TRP K 257 HIS 0.006 0.001 HIS K 204 Details of bonding type rmsd covalent geometry : bond 0.00400 (36244) covalent geometry : angle 0.64041 (50838) hydrogen bonds : bond 0.04517 ( 1173) hydrogen bonds : angle 4.81706 ( 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 407 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 330 time to evaluate : 0.802 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 183 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7201 (tpt-90) REVERT: C 230 CYS cc_start: 0.7508 (m) cc_final: 0.6650 (p) REVERT: C 260 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: C 316 MET cc_start: 0.7635 (mtm) cc_final: 0.7433 (mpp) REVERT: D 83 ASP cc_start: 0.8186 (m-30) cc_final: 0.7942 (t70) REVERT: D 132 ASN cc_start: 0.8903 (p0) cc_final: 0.8660 (p0) REVERT: F 42 SER cc_start: 0.8528 (m) cc_final: 0.8217 (p) REVERT: G 168 GLN cc_start: 0.9241 (tp40) cc_final: 0.9038 (mm110) REVERT: G 181 PHE cc_start: 0.8728 (m-80) cc_final: 0.8509 (m-80) REVERT: G 201 GLU cc_start: 0.8272 (mp0) cc_final: 0.7877 (pm20) REVERT: G 204 MET cc_start: 0.8037 (tmm) cc_final: 0.7672 (tmm) REVERT: G 316 MET cc_start: 0.8034 (mmp) cc_final: 0.7545 (mmp) REVERT: H 119 GLN cc_start: 0.9280 (mt0) cc_final: 0.9031 (mm110) REVERT: H 121 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (mtt90) REVERT: H 123 PHE cc_start: 0.8456 (p90) cc_final: 0.8067 (p90) REVERT: H 125 PHE cc_start: 0.8062 (p90) cc_final: 0.7789 (p90) REVERT: I 128 MET cc_start: 0.8526 (tmm) cc_final: 0.7796 (tmm) REVERT: J 49 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7985 (mmtt) REVERT: J 55 LEU cc_start: 0.8425 (mt) cc_final: 0.8081 (mt) REVERT: K 197 ASN cc_start: 0.7691 (m-40) cc_final: 0.6998 (t0) REVERT: K 235 MET cc_start: 0.5145 (ttt) cc_final: 0.4170 (tmm) REVERT: K 268 PHE cc_start: 0.8155 (m-80) cc_final: 0.7147 (m-80) REVERT: K 292 LEU cc_start: 0.9335 (tp) cc_final: 0.8676 (pp) REVERT: c 183 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7207 (tpt-90) REVERT: c 230 CYS cc_start: 0.7524 (m) cc_final: 0.6658 (p) REVERT: c 260 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: d 83 ASP cc_start: 0.8172 (m-30) cc_final: 0.7867 (t70) REVERT: e 62 ARG cc_start: 0.7508 (mmm-85) cc_final: 0.7013 (mmm-85) REVERT: f 42 SER cc_start: 0.8532 (m) cc_final: 0.8237 (p) REVERT: g 168 GLN cc_start: 0.9235 (tp40) cc_final: 0.9035 (mm110) REVERT: g 181 PHE cc_start: 0.8722 (m-80) cc_final: 0.8471 (m-80) REVERT: g 201 GLU cc_start: 0.8262 (mp0) cc_final: 0.7879 (pm20) REVERT: g 204 MET cc_start: 0.8058 (tmm) cc_final: 0.7663 (tmm) REVERT: g 316 MET cc_start: 0.8039 (mmp) cc_final: 0.7560 (mmp) REVERT: h 119 GLN cc_start: 0.9281 (mt0) cc_final: 0.9024 (mm110) REVERT: h 121 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8162 (mtt90) REVERT: h 125 PHE cc_start: 0.8062 (p90) cc_final: 0.7748 (p90) REVERT: i 128 MET cc_start: 0.8532 (tmm) cc_final: 0.7825 (tmm) REVERT: j 49 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7977 (mmtt) REVERT: j 55 LEU cc_start: 0.8445 (mt) cc_final: 0.8104 (mt) REVERT: k 197 ASN cc_start: 0.7708 (m-40) cc_final: 0.7023 (t0) REVERT: k 235 MET cc_start: 0.5171 (ttt) cc_final: 0.4191 (tmm) REVERT: k 268 PHE cc_start: 0.8101 (m-80) cc_final: 0.7074 (m-80) REVERT: k 292 LEU cc_start: 0.9348 (tp) cc_final: 0.8685 (pp) outliers start: 77 outliers final: 40 residues processed: 382 average time/residue: 0.2157 time to fit residues: 130.8582 Evaluate side-chains 324 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 335 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 D residue 95 VAL 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 199 ILE Chi-restraints excluded: chain G residue 218 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 J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 244 GLN Chi-restraints excluded: chain c residue 260 MET Chi-restraints excluded: chain c residue 335 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 d residue 95 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 199 ILE Chi-restraints excluded: chain g residue 218 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 j residue 3 LEU Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 49 LYS 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: 8.9990 chunk 261 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 270 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 270 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 GLN c 244 GLN ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 HIS ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.069038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.049274 restraints weight = 229071.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050629 restraints weight = 120878.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051425 restraints weight = 81988.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051910 restraints weight = 65778.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.052180 restraints weight = 57929.581| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 36244 Z= 0.229 Angle : 0.707 18.772 50838 Z= 0.345 Chirality : 0.041 0.167 5938 Planarity : 0.005 0.044 5096 Dihedral : 20.115 108.176 9664 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.64 % Allowed : 13.46 % Favored : 83.90 % 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 aren not related in a simple way. whole: -0.63 (0.14), residues: 3296 helix: 0.11 (0.18), residues: 774 sheet: -1.44 (0.18), residues: 732 loop : -0.03 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 114 TYR 0.022 0.002 TYR j 15 PHE 0.023 0.002 PHE d 125 TRP 0.010 0.002 TRP k 177 HIS 0.008 0.002 HIS G 103 Details of bonding type rmsd covalent geometry : bond 0.00514 (36244) covalent geometry : angle 0.70653 (50838) hydrogen bonds : bond 0.05523 ( 1173) hydrogen bonds : angle 4.94528 ( 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 399 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 1.228 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: C 182 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: C 183 ARG cc_start: 0.8267 (ttt180) cc_final: 0.7742 (tpt-90) REVERT: C 229 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8804 (mt) REVERT: C 245 GLU cc_start: 0.6776 (pt0) cc_final: 0.6369 (pt0) REVERT: D 83 ASP cc_start: 0.8343 (m-30) cc_final: 0.7895 (t70) REVERT: D 140 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8888 (tmmt) REVERT: E 42 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8362 (tpp-160) REVERT: E 61 ARG cc_start: 0.7017 (mmp-170) cc_final: 0.6258 (mmm-85) REVERT: E 62 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7339 (mmm-85) REVERT: E 79 MET cc_start: 0.8123 (ttp) cc_final: 0.6936 (ptm) REVERT: E 105 TYR cc_start: 0.9051 (p90) cc_final: 0.8486 (p90) REVERT: F 42 SER cc_start: 0.8617 (m) cc_final: 0.8145 (t) REVERT: G 175 THR cc_start: 0.9324 (m) cc_final: 0.9044 (m) REVERT: G 316 MET cc_start: 0.8126 (mmp) cc_final: 0.7663 (mmp) REVERT: H 119 GLN cc_start: 0.9330 (mt0) cc_final: 0.9020 (mm110) REVERT: J 49 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8281 (mmtp) REVERT: J 55 LEU cc_start: 0.8491 (mt) cc_final: 0.8194 (mt) REVERT: K 197 ASN cc_start: 0.7372 (m-40) cc_final: 0.6725 (t0) REVERT: K 220 MET cc_start: 0.7385 (tpp) cc_final: 0.6818 (tpp) REVERT: K 235 MET cc_start: 0.5481 (ttt) cc_final: 0.4534 (tmm) REVERT: K 268 PHE cc_start: 0.8189 (m-80) cc_final: 0.7275 (m-80) REVERT: K 292 LEU cc_start: 0.9311 (tp) cc_final: 0.8634 (pp) REVERT: K 320 LYS cc_start: 0.8996 (mttm) cc_final: 0.8764 (ptpp) REVERT: c 182 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: c 183 ARG cc_start: 0.8209 (ttt180) cc_final: 0.7699 (tpt-90) REVERT: c 229 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8798 (mt) REVERT: d 83 ASP cc_start: 0.8342 (m-30) cc_final: 0.7894 (t70) REVERT: d 120 LEU cc_start: 0.8916 (mp) cc_final: 0.8707 (mt) REVERT: d 123 PHE cc_start: 0.6429 (p90) cc_final: 0.5994 (p90) REVERT: d 133 MET cc_start: 0.6877 (mmm) cc_final: 0.6216 (mmm) REVERT: e 42 ARG cc_start: 0.8851 (tpp-160) cc_final: 0.8375 (tpp-160) REVERT: e 62 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.6451 (mmm-85) REVERT: e 66 GLU cc_start: 0.7504 (tt0) cc_final: 0.7062 (tt0) REVERT: e 79 MET cc_start: 0.8154 (ttm) cc_final: 0.7700 (ttp) REVERT: e 98 CYS cc_start: 0.9081 (m) cc_final: 0.8396 (m) REVERT: f 42 SER cc_start: 0.8647 (m) cc_final: 0.8170 (t) REVERT: g 175 THR cc_start: 0.9328 (m) cc_final: 0.9050 (m) REVERT: g 316 MET cc_start: 0.8120 (mmp) cc_final: 0.7671 (mmp) REVERT: h 119 GLN cc_start: 0.9304 (mt0) cc_final: 0.9017 (mm110) REVERT: h 123 PHE cc_start: 0.8395 (p90) cc_final: 0.8064 (p90) REVERT: j 49 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8274 (mmtp) REVERT: j 55 LEU cc_start: 0.8521 (mt) cc_final: 0.8282 (mt) REVERT: k 197 ASN cc_start: 0.7388 (m-40) cc_final: 0.6752 (t0) REVERT: k 220 MET cc_start: 0.7424 (tpp) cc_final: 0.6843 (tpp) REVERT: k 235 MET cc_start: 0.5498 (ttt) cc_final: 0.4560 (tmm) REVERT: k 268 PHE cc_start: 0.8176 (m-80) cc_final: 0.7270 (m-80) REVERT: k 292 LEU cc_start: 0.9314 (tp) cc_final: 0.8637 (pp) REVERT: k 320 LYS cc_start: 0.8996 (mttm) cc_final: 0.8765 (ptpp) outliers start: 78 outliers final: 48 residues processed: 378 average time/residue: 0.1992 time to fit residues: 122.1834 Evaluate side-chains 339 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 135 CYS 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 273 TYR Chi-restraints excluded: chain G residue 362 ILE 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 136 SER Chi-restraints excluded: chain H residue 154 LEU 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 Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 182 GLN Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 335 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain e residue 51 ILE 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 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 218 VAL Chi-restraints excluded: chain g residue 273 TYR Chi-restraints excluded: chain g residue 362 ILE 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 136 SER Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 310 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 164 optimal weight: 50.0000 chunk 266 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS ** 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** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 270 GLN d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.070504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050887 restraints weight = 223676.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.052273 restraints weight = 115954.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.053140 restraints weight = 78438.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.053644 restraints weight = 62338.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053890 restraints weight = 54664.473| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36244 Z= 0.114 Angle : 0.581 16.757 50838 Z= 0.285 Chirality : 0.037 0.149 5938 Planarity : 0.004 0.056 5096 Dihedral : 19.878 108.249 9664 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.03 % Allowed : 14.95 % Favored : 83.02 % 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 aren not related in a simple way. whole: -0.29 (0.15), residues: 3296 helix: 0.52 (0.19), residues: 776 sheet: -1.18 (0.18), residues: 718 loop : 0.07 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 114 TYR 0.018 0.001 TYR F 41 PHE 0.017 0.001 PHE d 125 TRP 0.009 0.001 TRP C 108 HIS 0.008 0.001 HIS k 204 Details of bonding type rmsd covalent geometry : bond 0.00259 (36244) covalent geometry : angle 0.58070 (50838) hydrogen bonds : bond 0.03523 ( 1173) hydrogen bonds : angle 4.45116 ( 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 390 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 330 time to evaluate : 1.207 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: C 182 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: C 350 MET cc_start: 0.7225 (mtt) cc_final: 0.7013 (mpp) REVERT: D 83 ASP cc_start: 0.8051 (m-30) cc_final: 0.7721 (t70) REVERT: D 120 LEU cc_start: 0.8836 (mt) cc_final: 0.8034 (pt) REVERT: D 129 LEU cc_start: 0.5152 (mt) cc_final: 0.4898 (tp) REVERT: D 132 ASN cc_start: 0.8925 (p0) cc_final: 0.8698 (p0) REVERT: E 42 ARG cc_start: 0.8793 (tpp-160) cc_final: 0.8239 (tpp-160) REVERT: E 62 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: E 79 MET cc_start: 0.8063 (ttp) cc_final: 0.7423 (ttp) REVERT: E 98 CYS cc_start: 0.8979 (m) cc_final: 0.8631 (m) REVERT: F 4 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7900 (mm110) REVERT: F 42 SER cc_start: 0.8741 (m) cc_final: 0.8131 (t) REVERT: F 49 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8560 (mtmm) REVERT: G 175 THR cc_start: 0.9070 (m) cc_final: 0.8799 (p) REVERT: G 316 MET cc_start: 0.8026 (mmp) cc_final: 0.7789 (mmp) REVERT: H 119 GLN cc_start: 0.9299 (mt0) cc_final: 0.9059 (mm-40) REVERT: H 125 PHE cc_start: 0.7791 (p90) cc_final: 0.7559 (p90) REVERT: J 49 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8172 (mmtt) REVERT: J 55 LEU cc_start: 0.8628 (mt) cc_final: 0.8401 (mt) REVERT: K 197 ASN cc_start: 0.7257 (m-40) cc_final: 0.6379 (t0) REVERT: K 220 MET cc_start: 0.7377 (tpp) cc_final: 0.7121 (tpp) REVERT: K 235 MET cc_start: 0.5258 (ttt) cc_final: 0.4333 (mtp) REVERT: K 268 PHE cc_start: 0.8045 (m-80) cc_final: 0.7072 (m-80) REVERT: K 292 LEU cc_start: 0.9299 (tp) cc_final: 0.8611 (pp) REVERT: K 320 LYS cc_start: 0.9000 (mttm) cc_final: 0.8756 (ptpp) REVERT: c 183 ARG cc_start: 0.8166 (ttt180) cc_final: 0.7785 (tpt-90) REVERT: c 316 MET cc_start: 0.7828 (mpp) cc_final: 0.7221 (mpp) REVERT: c 350 MET cc_start: 0.7209 (mtt) cc_final: 0.6993 (mpp) REVERT: d 83 ASP cc_start: 0.8019 (m-30) cc_final: 0.7806 (t70) REVERT: e 42 ARG cc_start: 0.8797 (tpp-160) cc_final: 0.8330 (tpp-160) REVERT: e 79 MET cc_start: 0.8036 (ttm) cc_final: 0.7322 (ttp) REVERT: e 98 CYS cc_start: 0.9019 (m) cc_final: 0.8216 (m) REVERT: e 99 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8598 (mt-10) REVERT: e 105 TYR cc_start: 0.8813 (p90) cc_final: 0.8168 (p90) REVERT: f 3 LEU cc_start: 0.8869 (tp) cc_final: 0.8471 (mt) REVERT: f 4 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8007 (mm110) REVERT: f 42 SER cc_start: 0.8742 (m) cc_final: 0.8154 (t) REVERT: f 49 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8563 (mtmm) REVERT: g 94 LEU cc_start: 0.8351 (tp) cc_final: 0.8130 (tt) REVERT: g 175 THR cc_start: 0.9071 (m) cc_final: 0.8803 (p) REVERT: g 316 MET cc_start: 0.8030 (mmp) cc_final: 0.7811 (mmp) REVERT: h 119 GLN cc_start: 0.9274 (mt0) cc_final: 0.9056 (mm-40) REVERT: h 121 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8018 (mtt90) REVERT: j 49 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8164 (mmtt) REVERT: j 55 LEU cc_start: 0.8587 (mt) cc_final: 0.8368 (mt) REVERT: k 197 ASN cc_start: 0.7280 (m-40) cc_final: 0.6406 (t0) REVERT: k 220 MET cc_start: 0.7238 (tpp) cc_final: 0.6990 (tpp) REVERT: k 235 MET cc_start: 0.5333 (ttt) cc_final: 0.4424 (mtp) REVERT: k 268 PHE cc_start: 0.8041 (m-80) cc_final: 0.7086 (m-80) REVERT: k 292 LEU cc_start: 0.9301 (tp) cc_final: 0.8610 (pp) REVERT: k 320 LYS cc_start: 0.9000 (mttm) cc_final: 0.8762 (ptpp) outliers start: 60 outliers final: 34 residues processed: 370 average time/residue: 0.1990 time to fit residues: 118.4588 Evaluate side-chains 309 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 135 CYS 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 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 136 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 335 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain g residue 135 CYS 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 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 136 SER Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain j residue 10 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 131 optimal weight: 30.0000 chunk 355 optimal weight: 30.0000 chunk 354 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 303 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 102 ASN E 136 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN J 10 GLN ** d 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN e 136 GLN ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.067941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048451 restraints weight = 227672.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049749 restraints weight = 119808.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050546 restraints weight = 82143.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051011 restraints weight = 65978.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051312 restraints weight = 58385.822| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 36244 Z= 0.237 Angle : 0.686 19.895 50838 Z= 0.339 Chirality : 0.040 0.157 5938 Planarity : 0.005 0.049 5096 Dihedral : 20.126 117.123 9664 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.74 % Allowed : 15.60 % Favored : 81.66 % 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 aren not related in a simple way. whole: -0.51 (0.15), residues: 3296 helix: 0.32 (0.19), residues: 774 sheet: -1.29 (0.18), residues: 736 loop : -0.06 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 114 TYR 0.019 0.002 TYR J 15 PHE 0.020 0.002 PHE h 123 TRP 0.008 0.001 TRP K 161 HIS 0.010 0.002 HIS g 103 Details of bonding type rmsd covalent geometry : bond 0.00531 (36244) covalent geometry : angle 0.68605 (50838) hydrogen bonds : bond 0.05361 ( 1173) hydrogen bonds : angle 4.87620 ( 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 354 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 273 time to evaluate : 0.981 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: C 182 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: C 316 MET cc_start: 0.7753 (mpp) cc_final: 0.7308 (mpp) REVERT: D 83 ASP cc_start: 0.8138 (m-30) cc_final: 0.7601 (t70) REVERT: D 123 PHE cc_start: 0.6680 (p90) cc_final: 0.6183 (p90) REVERT: D 129 LEU cc_start: 0.5139 (mt) cc_final: 0.4882 (tp) REVERT: D 133 MET cc_start: 0.7032 (mmm) cc_final: 0.6748 (mmm) REVERT: E 62 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7588 (tpp80) REVERT: F 42 SER cc_start: 0.8898 (m) cc_final: 0.8332 (t) REVERT: G 204 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7989 (tmm) REVERT: G 316 MET cc_start: 0.8136 (mmp) cc_final: 0.7630 (mmp) REVERT: J 49 LYS cc_start: 0.8494 (mmtm) cc_final: 0.7709 (mmtp) REVERT: J 55 LEU cc_start: 0.8620 (mt) cc_final: 0.8372 (mt) REVERT: K 220 MET cc_start: 0.7570 (tpp) cc_final: 0.7170 (tpp) REVERT: K 235 MET cc_start: 0.5543 (ttt) cc_final: 0.4561 (tmm) REVERT: K 268 PHE cc_start: 0.8091 (m-80) cc_final: 0.7176 (m-80) REVERT: K 292 LEU cc_start: 0.9342 (tp) cc_final: 0.8643 (pp) REVERT: c 182 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: c 183 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7861 (ttt90) REVERT: c 316 MET cc_start: 0.7862 (mpp) cc_final: 0.7267 (mpp) REVERT: d 83 ASP cc_start: 0.8275 (m-30) cc_final: 0.7823 (t70) REVERT: d 120 LEU cc_start: 0.8913 (mp) cc_final: 0.8710 (mt) REVERT: d 123 PHE cc_start: 0.6615 (p90) cc_final: 0.6175 (p90) REVERT: d 132 ASN cc_start: 0.8897 (p0) cc_final: 0.8542 (p0) REVERT: d 133 MET cc_start: 0.7085 (mmm) cc_final: 0.6708 (mmm) REVERT: e 42 ARG cc_start: 0.8726 (tpp-160) cc_final: 0.8199 (tpp-160) REVERT: e 45 ARG cc_start: 0.9069 (tpp-160) cc_final: 0.8709 (mmm160) REVERT: e 61 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6573 (mmm160) REVERT: e 70 PHE cc_start: 0.8654 (m-80) cc_final: 0.8433 (m-80) REVERT: e 79 MET cc_start: 0.8089 (ttm) cc_final: 0.7510 (ttp) REVERT: e 98 CYS cc_start: 0.9024 (m) cc_final: 0.8203 (m) REVERT: e 99 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8573 (mt-10) REVERT: e 105 TYR cc_start: 0.8924 (p90) cc_final: 0.8318 (p90) REVERT: f 42 SER cc_start: 0.8860 (m) cc_final: 0.8291 (t) REVERT: f 49 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8646 (mtmm) REVERT: g 94 LEU cc_start: 0.8366 (tp) cc_final: 0.8118 (tt) REVERT: g 316 MET cc_start: 0.8143 (mmp) cc_final: 0.7643 (mmp) REVERT: j 49 LYS cc_start: 0.8489 (mmtm) cc_final: 0.7715 (mmtp) REVERT: j 55 LEU cc_start: 0.8615 (mt) cc_final: 0.8370 (mt) REVERT: k 220 MET cc_start: 0.7491 (tpp) cc_final: 0.7062 (tpp) REVERT: k 235 MET cc_start: 0.5559 (ttt) cc_final: 0.4555 (tmm) REVERT: k 268 PHE cc_start: 0.8087 (m-80) cc_final: 0.7183 (m-80) REVERT: k 292 LEU cc_start: 0.9352 (tp) cc_final: 0.8649 (pp) REVERT: k 320 LYS cc_start: 0.9031 (mttm) cc_final: 0.8831 (ptpp) outliers start: 81 outliers final: 55 residues processed: 332 average time/residue: 0.2019 time to fit residues: 107.4227 Evaluate side-chains 306 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain G residue 94 LEU 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 199 ILE Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 273 TYR 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 H residue 136 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 182 GLN 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 51 ILE Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 273 TYR 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 136 SER Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 10 GLN 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: 0.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 326 optimal weight: 50.0000 chunk 294 optimal weight: 5.9990 chunk 337 optimal weight: 30.0000 chunk 318 optimal weight: 50.0000 chunk 137 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.068683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.049068 restraints weight = 231798.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050397 restraints weight = 120773.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051209 restraints weight = 82316.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.051663 restraints weight = 66206.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.051949 restraints weight = 58762.192| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 36244 Z= 0.170 Angle : 0.623 18.487 50838 Z= 0.305 Chirality : 0.038 0.154 5938 Planarity : 0.005 0.048 5096 Dihedral : 20.050 119.403 9664 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.23 % Allowed : 16.75 % Favored : 81.02 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3296 helix: 0.49 (0.19), residues: 772 sheet: -1.25 (0.19), residues: 712 loop : -0.07 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 114 TYR 0.017 0.002 TYR E 107 PHE 0.017 0.001 PHE H 123 TRP 0.010 0.001 TRP G 217 HIS 0.008 0.001 HIS K 204 Details of bonding type rmsd covalent geometry : bond 0.00388 (36244) covalent geometry : angle 0.62312 (50838) hydrogen bonds : bond 0.04164 ( 1173) hydrogen bonds : angle 4.67552 ( 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 352 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 1.282 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 182 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: D 83 ASP cc_start: 0.8195 (m-30) cc_final: 0.7870 (t70) REVERT: D 123 PHE cc_start: 0.6692 (p90) cc_final: 0.6180 (p90) REVERT: D 132 ASN cc_start: 0.8964 (p0) cc_final: 0.8563 (p0) REVERT: D 133 MET cc_start: 0.7352 (mmm) cc_final: 0.6832 (mmm) REVERT: E 75 GLU cc_start: 0.7750 (mp0) cc_final: 0.7406 (pp20) REVERT: E 99 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8401 (mt-10) REVERT: G 175 THR cc_start: 0.9247 (m) cc_final: 0.9017 (p) REVERT: G 181 PHE cc_start: 0.8894 (m-10) cc_final: 0.8504 (m-10) REVERT: G 260 MET cc_start: 0.8386 (tpp) cc_final: 0.8119 (tpt) REVERT: G 316 MET cc_start: 0.8099 (mmp) cc_final: 0.7522 (mmp) REVERT: I 36 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: J 49 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7623 (mmtp) REVERT: J 55 LEU cc_start: 0.8673 (mt) cc_final: 0.8440 (mt) REVERT: K 235 MET cc_start: 0.5314 (ttt) cc_final: 0.4290 (tmm) REVERT: K 268 PHE cc_start: 0.7976 (m-80) cc_final: 0.7034 (m-80) REVERT: K 292 LEU cc_start: 0.9348 (tp) cc_final: 0.8640 (pp) REVERT: c 182 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: c 183 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7865 (ttt180) REVERT: c 316 MET cc_start: 0.7910 (mpp) cc_final: 0.7154 (mpp) REVERT: d 83 ASP cc_start: 0.8150 (m-30) cc_final: 0.7678 (t70) REVERT: d 123 PHE cc_start: 0.6776 (p90) cc_final: 0.6276 (p90) REVERT: d 127 VAL cc_start: 0.6698 (t) cc_final: 0.6385 (t) REVERT: e 70 PHE cc_start: 0.8652 (m-80) cc_final: 0.8199 (m-80) REVERT: e 79 MET cc_start: 0.7990 (ttm) cc_final: 0.7351 (ttp) REVERT: e 98 CYS cc_start: 0.8989 (m) cc_final: 0.8110 (m) REVERT: e 105 TYR cc_start: 0.8870 (p90) cc_final: 0.8132 (p90) REVERT: f 42 SER cc_start: 0.8944 (m) cc_final: 0.8737 (m) REVERT: f 49 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8650 (mtmm) REVERT: g 175 THR cc_start: 0.9286 (m) cc_final: 0.9003 (p) REVERT: g 181 PHE cc_start: 0.8877 (m-10) cc_final: 0.8549 (m-10) REVERT: g 316 MET cc_start: 0.8100 (mmp) cc_final: 0.7545 (mmp) REVERT: i 36 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: j 49 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7663 (mmtp) REVERT: j 55 LEU cc_start: 0.8674 (mt) cc_final: 0.8439 (mt) REVERT: k 235 MET cc_start: 0.5323 (ttt) cc_final: 0.4311 (tmm) REVERT: k 268 PHE cc_start: 0.7962 (m-80) cc_final: 0.7050 (m-80) REVERT: k 292 LEU cc_start: 0.9357 (tp) cc_final: 0.8644 (pp) outliers start: 66 outliers final: 49 residues processed: 334 average time/residue: 0.2104 time to fit residues: 112.8651 Evaluate side-chains 312 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL 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 362 ILE 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 136 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 182 GLN Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 335 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL 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 362 ILE 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 136 SER Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 10 GLN 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: 8.9990 chunk 303 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 333 optimal weight: 30.0000 chunk 338 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 HIS D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN d 155 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.067866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048470 restraints weight = 229878.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049815 restraints weight = 120111.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050609 restraints weight = 81465.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.051069 restraints weight = 65266.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051294 restraints weight = 57699.451| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 36244 Z= 0.205 Angle : 0.662 19.065 50838 Z= 0.325 Chirality : 0.039 0.164 5938 Planarity : 0.005 0.052 5096 Dihedral : 20.125 121.075 9664 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.50 % Allowed : 17.69 % Favored : 79.80 % 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 aren not related in a simple way. whole: -0.52 (0.15), residues: 3296 helix: 0.40 (0.19), residues: 770 sheet: -1.23 (0.20), residues: 680 loop : -0.19 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 114 TYR 0.016 0.002 TYR j 15 PHE 0.022 0.002 PHE h 123 TRP 0.009 0.001 TRP k 440 HIS 0.009 0.001 HIS K 204 Details of bonding type rmsd covalent geometry : bond 0.00465 (36244) covalent geometry : angle 0.66206 (50838) hydrogen bonds : bond 0.04747 ( 1173) hydrogen bonds : angle 4.78008 ( 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: 74 poor density : 263 time to evaluate : 1.140 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: C 182 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: C 268 ASP cc_start: 0.8738 (m-30) cc_final: 0.8419 (m-30) REVERT: C 316 MET cc_start: 0.7783 (mpp) cc_final: 0.7210 (mpp) REVERT: D 83 ASP cc_start: 0.8421 (m-30) cc_final: 0.7893 (t70) REVERT: D 123 PHE cc_start: 0.6927 (p90) cc_final: 0.6395 (p90) REVERT: D 132 ASN cc_start: 0.8996 (p0) cc_final: 0.8630 (p0) REVERT: D 133 MET cc_start: 0.7412 (mmm) cc_final: 0.7109 (mmm) REVERT: E 62 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7536 (tpp80) REVERT: E 99 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8315 (mt-10) REVERT: G 181 PHE cc_start: 0.8995 (m-10) cc_final: 0.8593 (m-10) REVERT: G 316 MET cc_start: 0.8129 (mmp) cc_final: 0.7570 (mmp) REVERT: H 133 MET cc_start: 0.7198 (tpp) cc_final: 0.6994 (tpp) REVERT: I 36 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: J 49 LYS cc_start: 0.8506 (mmtm) cc_final: 0.7706 (mmtp) REVERT: J 55 LEU cc_start: 0.8747 (mt) cc_final: 0.8515 (mt) REVERT: K 235 MET cc_start: 0.5435 (ttt) cc_final: 0.4427 (tmm) REVERT: K 268 PHE cc_start: 0.8017 (m-80) cc_final: 0.7161 (m-80) REVERT: K 292 LEU cc_start: 0.9369 (tp) cc_final: 0.8718 (pp) REVERT: c 182 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: c 183 ARG cc_start: 0.8434 (ttt180) cc_final: 0.7477 (ttt90) REVERT: c 316 MET cc_start: 0.7873 (mpp) cc_final: 0.7120 (mpp) REVERT: d 83 ASP cc_start: 0.8507 (m-30) cc_final: 0.7980 (t70) REVERT: d 123 PHE cc_start: 0.6994 (p90) cc_final: 0.6437 (p90) REVERT: d 125 PHE cc_start: 0.8563 (p90) cc_final: 0.8322 (p90) REVERT: e 61 ARG cc_start: 0.7095 (mmm160) cc_final: 0.6280 (tpp80) REVERT: e 79 MET cc_start: 0.8083 (ttm) cc_final: 0.7355 (ttp) REVERT: e 98 CYS cc_start: 0.8995 (m) cc_final: 0.8129 (m) REVERT: e 105 TYR cc_start: 0.8925 (p90) cc_final: 0.8236 (p90) REVERT: e 128 MET cc_start: 0.8430 (tpp) cc_final: 0.7735 (tpp) REVERT: g 175 THR cc_start: 0.9343 (m) cc_final: 0.9114 (p) REVERT: g 181 PHE cc_start: 0.8904 (m-10) cc_final: 0.8497 (m-10) REVERT: g 260 MET cc_start: 0.8423 (tpp) cc_final: 0.8096 (tpp) REVERT: g 316 MET cc_start: 0.8134 (mmp) cc_final: 0.7592 (mmp) REVERT: h 123 PHE cc_start: 0.8540 (p90) cc_final: 0.8289 (p90) REVERT: h 133 MET cc_start: 0.7215 (tpp) cc_final: 0.7014 (tpp) REVERT: i 36 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: j 49 LYS cc_start: 0.8499 (mmtm) cc_final: 0.7724 (mmtp) REVERT: j 55 LEU cc_start: 0.8726 (mt) cc_final: 0.8473 (mt) REVERT: k 235 MET cc_start: 0.5420 (ttt) cc_final: 0.4438 (tmm) REVERT: k 268 PHE cc_start: 0.7970 (m-80) cc_final: 0.7106 (m-80) REVERT: k 292 LEU cc_start: 0.9374 (tp) cc_final: 0.8721 (pp) outliers start: 74 outliers final: 58 residues processed: 321 average time/residue: 0.2131 time to fit residues: 110.5564 Evaluate side-chains 304 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL 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 362 ILE 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 H residue 127 VAL Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 36 GLN 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 105 VAL Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 182 GLN Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 335 VAL Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 406 ASP Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 226 ILE Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 362 ILE 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 h residue 127 VAL Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain h residue 154 LEU Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain k residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 302 optimal weight: 50.0000 chunk 262 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 30.0000 chunk 126 optimal weight: 0.8980 chunk 336 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 342 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 153 optimal weight: 50.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 270 GLN d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.068464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.048962 restraints weight = 231292.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.050290 restraints weight = 120122.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.051106 restraints weight = 81751.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051582 restraints weight = 65588.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051843 restraints weight = 57955.837| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 36244 Z= 0.155 Angle : 0.627 17.996 50838 Z= 0.306 Chirality : 0.038 0.177 5938 Planarity : 0.005 0.056 5096 Dihedral : 20.023 120.027 9664 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.30 % Allowed : 18.03 % Favored : 79.67 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3296 helix: 0.52 (0.19), residues: 768 sheet: -1.19 (0.19), residues: 712 loop : -0.11 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 114 TYR 0.015 0.002 TYR E 107 PHE 0.019 0.001 PHE E 70 TRP 0.010 0.001 TRP k 440 HIS 0.009 0.001 HIS k 204 Details of bonding type rmsd covalent geometry : bond 0.00358 (36244) covalent geometry : angle 0.62733 (50838) hydrogen bonds : bond 0.04043 ( 1173) hydrogen bonds : angle 4.62797 ( 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 332 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 264 time to evaluate : 1.105 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: C 182 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: C 268 ASP cc_start: 0.8660 (m-30) cc_final: 0.8313 (m-30) REVERT: C 316 MET cc_start: 0.7808 (mpp) cc_final: 0.7198 (mpp) REVERT: D 83 ASP cc_start: 0.8115 (m-30) cc_final: 0.7470 (t70) REVERT: D 123 PHE cc_start: 0.6903 (p90) cc_final: 0.6340 (p90) REVERT: E 62 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7114 (mmm-85) REVERT: E 99 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8446 (mt-10) REVERT: F 40 LYS cc_start: 0.9183 (pptt) cc_final: 0.8814 (pptt) REVERT: G 175 THR cc_start: 0.9207 (m) cc_final: 0.8900 (p) REVERT: G 181 PHE cc_start: 0.8979 (m-10) cc_final: 0.8569 (m-10) REVERT: G 316 MET cc_start: 0.8106 (mmp) cc_final: 0.7514 (mmp) REVERT: I 36 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: J 49 LYS cc_start: 0.8481 (mmtm) cc_final: 0.7623 (mmtp) REVERT: J 55 LEU cc_start: 0.8703 (mt) cc_final: 0.8471 (mt) REVERT: K 235 MET cc_start: 0.5370 (ttt) cc_final: 0.4360 (tmm) REVERT: K 292 LEU cc_start: 0.9371 (tp) cc_final: 0.8740 (pp) REVERT: c 182 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: c 183 ARG cc_start: 0.8408 (ttt180) cc_final: 0.7754 (tpt-90) REVERT: c 268 ASP cc_start: 0.8675 (m-30) cc_final: 0.8368 (m-30) REVERT: c 316 MET cc_start: 0.7881 (mpp) cc_final: 0.7144 (mpp) REVERT: d 83 ASP cc_start: 0.8183 (m-30) cc_final: 0.7604 (t70) REVERT: d 123 PHE cc_start: 0.6865 (p90) cc_final: 0.6265 (p90) REVERT: d 128 LYS cc_start: 0.7016 (tttt) cc_final: 0.6508 (tptp) REVERT: e 79 MET cc_start: 0.7990 (ttm) cc_final: 0.7237 (ttp) REVERT: e 98 CYS cc_start: 0.8945 (m) cc_final: 0.8088 (m) REVERT: e 105 TYR cc_start: 0.8919 (p90) cc_final: 0.8234 (p90) REVERT: e 128 MET cc_start: 0.8406 (tpp) cc_final: 0.7746 (tpp) REVERT: g 175 THR cc_start: 0.9320 (m) cc_final: 0.9113 (p) REVERT: g 181 PHE cc_start: 0.8889 (m-10) cc_final: 0.8531 (m-10) REVERT: g 204 MET cc_start: 0.8181 (tmm) cc_final: 0.7933 (tmm) REVERT: g 260 MET cc_start: 0.8398 (tpp) cc_final: 0.8085 (tpp) REVERT: g 316 MET cc_start: 0.8105 (mmp) cc_final: 0.7529 (mmp) REVERT: h 121 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8343 (mtt90) REVERT: h 123 PHE cc_start: 0.8533 (p90) cc_final: 0.8268 (p90) REVERT: i 36 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: j 49 LYS cc_start: 0.8478 (mmtm) cc_final: 0.7624 (mmtp) REVERT: j 55 LEU cc_start: 0.8706 (mt) cc_final: 0.8471 (mt) REVERT: k 235 MET cc_start: 0.5386 (ttt) cc_final: 0.4376 (tmm) REVERT: k 268 PHE cc_start: 0.7933 (m-80) cc_final: 0.7030 (m-80) REVERT: k 292 LEU cc_start: 0.9372 (tp) cc_final: 0.8723 (pp) outliers start: 68 outliers final: 52 residues processed: 316 average time/residue: 0.2027 time to fit residues: 103.7351 Evaluate side-chains 305 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 157 VAL 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 362 ILE 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 127 VAL Chi-restraints excluded: chain H residue 154 LEU 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 K residue 264 LEU Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 182 GLN 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 132 ASN Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 94 LEU 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 226 ILE Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 362 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 282 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 292 optimal weight: 0.0570 chunk 248 optimal weight: 3.9990 chunk 329 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 159 optimal weight: 50.0000 chunk 195 optimal weight: 7.9990 chunk 351 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 chunk 335 optimal weight: 20.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 HIS D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.067826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.048294 restraints weight = 231589.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049602 restraints weight = 121093.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050402 restraints weight = 82740.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050858 restraints weight = 66404.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051149 restraints weight = 58767.317| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 36244 Z= 0.188 Angle : 0.660 18.678 50838 Z= 0.322 Chirality : 0.039 0.185 5938 Planarity : 0.005 0.101 5096 Dihedral : 20.088 120.266 9664 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.23 % Allowed : 18.40 % Favored : 79.36 % 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 aren not related in a simple way. whole: -0.44 (0.15), residues: 3296 helix: 0.44 (0.19), residues: 768 sheet: -1.12 (0.20), residues: 668 loop : -0.17 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 114 TYR 0.015 0.002 TYR g 323 PHE 0.022 0.002 PHE E 70 TRP 0.014 0.001 TRP k 257 HIS 0.009 0.001 HIS k 204 Details of bonding type rmsd covalent geometry : bond 0.00429 (36244) covalent geometry : angle 0.66020 (50838) hydrogen bonds : bond 0.04517 ( 1173) hydrogen bonds : angle 4.71230 ( 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 321 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 0.731 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: C 182 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: C 268 ASP cc_start: 0.8717 (m-30) cc_final: 0.8334 (m-30) REVERT: C 316 MET cc_start: 0.7770 (mpp) cc_final: 0.7179 (mpp) REVERT: D 82 ASP cc_start: 0.8929 (p0) cc_final: 0.8615 (p0) REVERT: D 83 ASP cc_start: 0.8727 (m-30) cc_final: 0.8396 (t70) REVERT: D 84 ILE cc_start: 0.8435 (pt) cc_final: 0.8193 (pt) REVERT: D 123 PHE cc_start: 0.7061 (p90) cc_final: 0.6378 (p90) REVERT: D 133 MET cc_start: 0.7747 (mmm) cc_final: 0.7371 (mtt) REVERT: E 62 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7044 (mmm-85) REVERT: E 99 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8463 (mt-10) REVERT: E 128 MET cc_start: 0.8436 (tpp) cc_final: 0.7995 (tpp) REVERT: F 40 LYS cc_start: 0.9186 (pptt) cc_final: 0.8813 (pptt) REVERT: G 175 THR cc_start: 0.9385 (m) cc_final: 0.9180 (p) REVERT: G 181 PHE cc_start: 0.8995 (m-10) cc_final: 0.8549 (m-10) REVERT: G 316 MET cc_start: 0.8123 (mmp) cc_final: 0.7595 (mmp) REVERT: J 49 LYS cc_start: 0.8530 (mmtm) cc_final: 0.7720 (mmtp) REVERT: J 55 LEU cc_start: 0.8746 (mt) cc_final: 0.8531 (mt) REVERT: K 220 MET cc_start: 0.7368 (tpp) cc_final: 0.7015 (tpp) REVERT: K 235 MET cc_start: 0.5499 (ttt) cc_final: 0.4490 (tmm) REVERT: K 268 PHE cc_start: 0.7421 (m-80) cc_final: 0.7039 (m-80) REVERT: K 292 LEU cc_start: 0.9379 (tp) cc_final: 0.8782 (pp) REVERT: c 182 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: c 183 ARG cc_start: 0.8432 (ttt180) cc_final: 0.7866 (tpt-90) REVERT: c 268 ASP cc_start: 0.8713 (m-30) cc_final: 0.8411 (m-30) REVERT: c 316 MET cc_start: 0.7855 (mpp) cc_final: 0.7142 (mpp) REVERT: d 82 ASP cc_start: 0.8948 (p0) cc_final: 0.8690 (p0) REVERT: d 123 PHE cc_start: 0.7118 (p90) cc_final: 0.6410 (p90) REVERT: d 128 LYS cc_start: 0.6981 (tttt) cc_final: 0.6500 (tmtt) REVERT: e 61 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7393 (tpp80) REVERT: e 79 MET cc_start: 0.7956 (ttm) cc_final: 0.7208 (ttp) REVERT: e 98 CYS cc_start: 0.8972 (m) cc_final: 0.8141 (m) REVERT: e 105 TYR cc_start: 0.8926 (p90) cc_final: 0.8285 (p90) REVERT: e 128 MET cc_start: 0.8473 (tpp) cc_final: 0.7920 (tpp) REVERT: f 39 ASP cc_start: 0.9228 (t0) cc_final: 0.9019 (t0) REVERT: g 175 THR cc_start: 0.9343 (m) cc_final: 0.9140 (p) REVERT: g 181 PHE cc_start: 0.8896 (m-10) cc_final: 0.8523 (m-10) REVERT: g 260 MET cc_start: 0.8405 (tpp) cc_final: 0.8148 (tpp) REVERT: g 316 MET cc_start: 0.8132 (mmp) cc_final: 0.7609 (mmp) REVERT: h 123 PHE cc_start: 0.8533 (p90) cc_final: 0.8228 (p90) REVERT: j 49 LYS cc_start: 0.8523 (mmtm) cc_final: 0.7717 (mmtp) REVERT: j 55 LEU cc_start: 0.8761 (mt) cc_final: 0.8530 (mt) REVERT: k 220 MET cc_start: 0.7348 (tpp) cc_final: 0.7000 (tpp) REVERT: k 235 MET cc_start: 0.5509 (ttt) cc_final: 0.4508 (tmm) REVERT: k 268 PHE cc_start: 0.7969 (m-80) cc_final: 0.7474 (m-80) REVERT: k 292 LEU cc_start: 0.9378 (tp) cc_final: 0.8773 (pp) outliers start: 66 outliers final: 52 residues processed: 307 average time/residue: 0.2010 time to fit residues: 100.0233 Evaluate side-chains 295 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 106 VAL 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 180 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 362 ILE 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 127 VAL Chi-restraints excluded: chain H residue 154 LEU 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 105 VAL Chi-restraints excluded: chain c residue 151 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 182 GLN 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 132 ASN Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 135 CYS Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 199 ILE Chi-restraints excluded: chain g residue 226 ILE Chi-restraints excluded: chain g residue 253 VAL Chi-restraints excluded: chain g residue 362 ILE 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 h residue 154 LEU Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain j residue 12 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 65 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 350 optimal weight: 20.0000 chunk 329 optimal weight: 50.0000 chunk 200 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 HIS d 155 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.067708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.048403 restraints weight = 230335.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049716 restraints weight = 120903.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.050514 restraints weight = 82734.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.050991 restraints weight = 66408.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051219 restraints weight = 58632.939| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 36244 Z= 0.179 Angle : 0.649 17.951 50838 Z= 0.316 Chirality : 0.039 0.175 5938 Planarity : 0.005 0.114 5096 Dihedral : 20.082 120.644 9664 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.13 % Allowed : 18.81 % Favored : 79.06 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3296 helix: 0.42 (0.19), residues: 770 sheet: -1.08 (0.20), residues: 686 loop : -0.12 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG e 62 TYR 0.014 0.002 TYR G 323 PHE 0.025 0.002 PHE h 123 TRP 0.010 0.001 TRP k 440 HIS 0.009 0.001 HIS k 204 Details of bonding type rmsd covalent geometry : bond 0.00408 (36244) covalent geometry : angle 0.64859 (50838) hydrogen bonds : bond 0.04294 ( 1173) hydrogen bonds : angle 4.69268 ( 2839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6450.84 seconds wall clock time: 112 minutes 5.70 seconds (6725.70 seconds total)