Starting phenix.real_space_refine on Thu Mar 21 00:12:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/03_2024/6pig_20350.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 59 5.49 5 S 142 5.16 5 C 18143 2.51 5 N 4990 2.21 5 O 5533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G ARG 503": "NH1" <-> "NH2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G GLU 530": "OE1" <-> "OE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G ARG 584": "NH1" <-> "NH2" Residue "G ARG 628": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 281": "NH1" <-> "NH2" Residue "I GLU 291": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I GLU 327": "OE1" <-> "OE2" Residue "I ARG 346": "NH1" <-> "NH2" Residue "I GLU 384": "OE1" <-> "OE2" Residue "I ARG 387": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 258": "OE1" <-> "OE2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J GLU 302": "OE1" <-> "OE2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J GLU 327": "OE1" <-> "OE2" Residue "J ARG 346": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28867 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4009 Classifications: {'peptide': 511} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1606 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 187} Chain: "I" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2923 Classifications: {'peptide': 357} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 3 Chain: "J" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2978 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Time building chain proxies: 15.05, per 1000 atoms: 0.52 Number of scatterers: 28867 At special positions: 0 Unit cell: (133, 161.5, 185.25, 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 142 16.00 P 59 15.00 O 5533 8.00 N 4990 7.00 C 18143 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 - 3.50 Amino acid : False - 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: 10.86 Conformation dependent library (CDL) restraints added in 4.9 seconds 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 36 sheets defined 26.7% alpha, 12.4% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 9.60 Creating SS restraints... Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.558A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.783A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.112A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 4.028A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.574A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.799A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.551A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.789A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.560A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.689A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.808A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.633A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.895A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.061A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.854A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.646A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.802A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.894A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.680A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.832A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.939A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.637A pdb=" N TYR D 316 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.797A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.809A pdb=" N ALA E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.683A pdb=" N GLN E 67 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.772A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.549A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.820A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.513A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 4.022A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.870A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.629A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.995A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.512A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 312' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.742A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 342 removed outlier: 3.749A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 36 through 44 removed outlier: 4.003A pdb=" N THR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.266A pdb=" N ASP G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.736A pdb=" N ILE G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 3.556A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 167 removed outlier: 3.918A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.735A pdb=" N MET G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 229 removed outlier: 4.023A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 229 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.892A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.919A pdb=" N SER G 499 " --> pdb=" O THR G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 529 Processing helix chain 'G' and resid 550 through 557 Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.798A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 70 removed outlier: 3.529A pdb=" N ASP H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 80 removed outlier: 3.593A pdb=" N GLN H 77 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.582A pdb=" N ARG H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 128 No H-bonds generated for 'chain 'H' and resid 126 through 128' Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.299A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE I 44 " --> pdb=" O PHE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 removed outlier: 4.386A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 201 removed outlier: 3.857A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 196 through 201' Processing helix chain 'I' and resid 216 through 228 removed outlier: 3.965A pdb=" N ARG I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.863A pdb=" N PHE I 251 " --> pdb=" O TRP I 247 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.950A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.901A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 333 Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.999A pdb=" N ALA I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 379 removed outlier: 3.502A pdb=" N ILE I 372 " --> pdb=" O HIS I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 24 removed outlier: 3.916A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.806A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.626A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 231 removed outlier: 4.151A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 removed outlier: 3.861A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.644A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'J' and resid 297 through 310 Processing helix chain 'J' and resid 328 through 333 removed outlier: 3.982A pdb=" N LEU J 332 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.556A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 206 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.909A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.848A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.718A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.719A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 156 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB7, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.893A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC3, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.606A pdb=" N VAL F 166 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 204 Processing sheet with id=AD1, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.590A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD3, first strand: chain 'G' and resid 539 through 541 Processing sheet with id=AD4, first strand: chain 'G' and resid 569 through 572 removed outlier: 3.878A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'H' and resid 55 through 56 removed outlier: 3.535A pdb=" N THR H 9 " --> pdb=" O HIS H 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS H 85 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AD9, first strand: chain 'J' and resid 322 through 324 753 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 11.78 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: 5482 1.33 - 1.46: 7938 1.46 - 1.58: 15985 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29728 Sorted by residual: bond pdb=" N ILE J 125 " pdb=" CA ILE J 125 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.50e-03 1.78e+04 2.22e+01 bond pdb=" N ILE E 190 " pdb=" CA ILE E 190 " ideal model delta sigma weight residual 1.459 1.500 -0.042 9.10e-03 1.21e+04 2.10e+01 bond pdb=" N VAL G 497 " pdb=" CA VAL G 497 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 2.01e+01 bond pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.99e+01 bond pdb=" N LEU H 11 " pdb=" CA LEU H 11 " ideal model delta sigma weight residual 1.463 1.494 -0.031 6.90e-03 2.10e+04 1.96e+01 ... (remaining 29723 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.11: 599 104.11 - 111.72: 11866 111.72 - 119.33: 15406 119.33 - 126.95: 12174 126.95 - 134.56: 582 Bond angle restraints: 40627 Sorted by residual: angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 96.50 6.75 1.05e+00 9.07e-01 4.13e+01 angle pdb=" N PRO C 276 " pdb=" CA PRO C 276 " pdb=" CB PRO C 276 " ideal model delta sigma weight residual 103.25 96.88 6.37 1.05e+00 9.07e-01 3.68e+01 angle pdb=" C GLN B 67 " pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 119.92 125.43 -5.51 9.60e-01 1.09e+00 3.29e+01 angle pdb=" CA ILE G 201 " pdb=" C ILE G 201 " pdb=" O ILE G 201 " ideal model delta sigma weight residual 121.68 117.44 4.24 7.90e-01 1.60e+00 2.88e+01 angle pdb=" C LYS D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta sigma weight residual 120.44 126.25 -5.81 1.09e+00 8.42e-01 2.84e+01 ... (remaining 40622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 17217 35.97 - 71.94: 504 71.94 - 107.91: 38 107.91 - 143.88: 2 143.88 - 179.85: 2 Dihedral angle restraints: 17763 sinusoidal: 7678 harmonic: 10085 Sorted by residual: dihedral pdb=" CA TRP A 24 " pdb=" C TRP A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta harmonic sigma weight residual 180.00 -100.77 -79.23 0 5.00e+00 4.00e-02 2.51e+02 dihedral pdb=" CA ILE I 125 " pdb=" C ILE I 125 " pdb=" N PRO I 126 " pdb=" CA PRO I 126 " ideal model delta harmonic sigma weight residual 180.00 110.99 69.01 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA LYS J 7 " pdb=" C LYS J 7 " pdb=" N PRO J 8 " pdb=" CA PRO J 8 " ideal model delta harmonic sigma weight residual -180.00 -125.64 -54.36 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 17760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2212 0.061 - 0.122: 1583 0.122 - 0.184: 588 0.184 - 0.245: 105 0.245 - 0.306: 1 Chirality restraints: 4489 Sorted by residual: chirality pdb=" CA HIS A 349 " pdb=" N HIS A 349 " pdb=" C HIS A 349 " pdb=" CB HIS A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' G 1 41 " pdb=" C3' G 1 41 " pdb=" O2' G 1 41 " pdb=" C1' G 1 41 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE B 85 " pdb=" N ILE B 85 " pdb=" C ILE B 85 " pdb=" CB ILE B 85 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4486 not shown) Planarity restraints: 4986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 48 " -0.017 2.00e-02 2.50e+03 1.47e-02 6.52e+00 pdb=" N9 G 1 48 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G 1 48 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 48 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 48 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G 1 48 " -0.029 2.00e-02 2.50e+03 pdb=" N1 G 1 48 " 0.026 2.00e-02 2.50e+03 pdb=" C2 G 1 48 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 48 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 1 48 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 125 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO I 126 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO I 126 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 126 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 67 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ASP H 67 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP H 67 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU H 68 " 0.015 2.00e-02 2.50e+03 ... (remaining 4983 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1033 2.72 - 3.26: 26356 3.26 - 3.81: 42513 3.81 - 4.35: 57282 4.35 - 4.90: 94986 Nonbonded interactions: 222170 Sorted by model distance: nonbonded pdb=" O GLU H 154 " pdb=" O PHE H 163 " model vdw 2.173 3.040 nonbonded pdb=" O LEU H 152 " pdb=" NH1 ARG H 164 " model vdw 2.327 2.520 nonbonded pdb=" O ASP A 14 " pdb=" NZ LYS G 510 " model vdw 2.348 2.520 nonbonded pdb=" O LYS G 517 " pdb=" N ILE G 519 " model vdw 2.356 2.520 nonbonded pdb=" O ASP G 608 " pdb=" OG1 THR G 611 " model vdw 2.377 2.440 ... (remaining 222165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 193 or resid 195 through 232 or resid 236 throug \ h 351 or resid 361 through 378 or resid 380 through 393)) selection = (chain 'J' and (resid 1 through 162 or resid 164 or resid 166 or resid 196 throu \ gh 351 or resid 361 through 378 or resid 380 through 393)) } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.420 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 78.190 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.014 0.047 29728 Z= 0.894 Angle : 1.756 8.247 40627 Z= 1.238 Chirality : 0.085 0.306 4489 Planarity : 0.004 0.063 4986 Dihedral : 16.960 179.853 11211 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 3.45 % Allowed : 15.16 % Favored : 81.39 % Rotamer: Outliers : 1.58 % Allowed : 8.37 % Favored : 90.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 6.06 % Twisted General : 1.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.12), residues: 3391 helix: -2.89 (0.13), residues: 868 sheet: -2.09 (0.21), residues: 484 loop : -3.87 (0.11), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 24 HIS 0.010 0.002 HIS A 349 PHE 0.017 0.002 PHE B 246 TYR 0.027 0.002 TYR H 149 ARG 0.005 0.001 ARG J 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 3.306 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8002 (tp30) cc_final: 0.7787 (tp30) REVERT: A 122 LYS cc_start: 0.7184 (tptt) cc_final: 0.6893 (tttp) REVERT: A 165 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7220 (mptt) REVERT: A 202 ASP cc_start: 0.6072 (m-30) cc_final: 0.5791 (m-30) REVERT: A 297 TYR cc_start: 0.8139 (m-80) cc_final: 0.7700 (m-10) REVERT: A 342 ILE cc_start: 0.8500 (mt) cc_final: 0.8216 (mm) REVERT: B 117 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 195 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7947 (mtmm) REVERT: B 338 MET cc_start: 0.8802 (mmt) cc_final: 0.8389 (mmt) REVERT: C 99 GLN cc_start: 0.8144 (mt0) cc_final: 0.7520 (mp10) REVERT: C 107 LYS cc_start: 0.7554 (tptt) cc_final: 0.7113 (tttt) REVERT: C 210 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7031 (ptp90) REVERT: D 107 LYS cc_start: 0.7996 (pttm) cc_final: 0.7546 (tmtt) REVERT: D 210 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7259 (ttp-110) REVERT: D 268 ILE cc_start: 0.8309 (pt) cc_final: 0.7718 (mt) REVERT: E 254 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7832 (mt-10) REVERT: F 74 ASP cc_start: 0.8815 (m-30) cc_final: 0.8501 (m-30) REVERT: F 122 LYS cc_start: 0.7908 (tptt) cc_final: 0.7516 (tptp) REVERT: F 210 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7243 (ttm170) REVERT: F 294 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (t) REVERT: F 311 GLN cc_start: 0.7757 (mt0) cc_final: 0.7445 (pp30) REVERT: G 177 MET cc_start: 0.5077 (ttt) cc_final: 0.4829 (tmm) REVERT: G 200 GLN cc_start: 0.7821 (mt0) cc_final: 0.7563 (mt0) REVERT: H 4 TYR cc_start: 0.6939 (m-80) cc_final: 0.6545 (m-80) REVERT: H 65 GLU cc_start: 0.7665 (tp30) cc_final: 0.7307 (tp30) REVERT: I 257 ASP cc_start: 0.6737 (p0) cc_final: 0.5875 (p0) REVERT: I 276 LYS cc_start: 0.5591 (mtmm) cc_final: 0.5220 (mttm) REVERT: I 294 LEU cc_start: 0.7529 (mt) cc_final: 0.6642 (mt) REVERT: I 322 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7252 (mtpt) REVERT: I 338 GLN cc_start: 0.8433 (mt0) cc_final: 0.8061 (mt0) REVERT: I 365 TYR cc_start: 0.7727 (m-80) cc_final: 0.7509 (m-80) REVERT: J 2 PHE cc_start: 0.8226 (t80) cc_final: 0.7783 (t80) REVERT: J 238 PHE cc_start: 0.6309 (t80) cc_final: 0.5920 (p90) REVERT: J 261 PHE cc_start: 0.3242 (t80) cc_final: 0.2323 (m-10) outliers start: 48 outliers final: 17 residues processed: 460 average time/residue: 0.4251 time to fit residues: 305.7791 Evaluate side-chains 300 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 533 PRO Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN A 312 GLN B 35 ASN B 145 ASN B 174 ASN B 183 ASN B 348 GLN C 104 ASN C 174 ASN C 179 GLN C 214 HIS C 311 GLN D 135 ASN D 183 ASN D 328 GLN E 99 GLN E 241 GLN E 311 GLN E 349 HIS F 174 ASN F 183 ASN G 227 GLN G 230 GLN G 246 ASN G 518 HIS G 618 ASN H 17 ASN H 162 ASN H 166 ASN I 60 ASN I 95 ASN I 154 ASN I 207 HIS J 23 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN J 313 GLN J 345 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29728 Z= 0.193 Angle : 0.756 12.851 40627 Z= 0.399 Chirality : 0.045 0.213 4489 Planarity : 0.005 0.078 4986 Dihedral : 15.644 179.611 4673 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.80 % Allowed : 14.48 % Favored : 84.72 % Rotamer: Outliers : 2.90 % Allowed : 12.39 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 5.45 % Twisted General : 1.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.13), residues: 3391 helix: -1.64 (0.16), residues: 929 sheet: -1.53 (0.23), residues: 488 loop : -3.59 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 24 HIS 0.007 0.001 HIS D 84 PHE 0.015 0.001 PHE I 238 TYR 0.029 0.001 TYR H 149 ARG 0.006 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 319 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.7884 (mpp) cc_final: 0.7655 (mpp) REVERT: B 102 LYS cc_start: 0.7310 (mtmt) cc_final: 0.6707 (mtpt) REVERT: B 117 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 195 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8239 (mtmm) REVERT: B 338 MET cc_start: 0.8836 (mmt) cc_final: 0.8636 (mmt) REVERT: C 99 GLN cc_start: 0.8160 (mt0) cc_final: 0.7469 (mp10) REVERT: C 107 LYS cc_start: 0.7638 (tptt) cc_final: 0.7161 (tttt) REVERT: C 210 ARG cc_start: 0.7802 (ptp-170) cc_final: 0.6957 (ptp90) REVERT: D 69 ASN cc_start: 0.8177 (p0) cc_final: 0.7968 (p0) REVERT: D 107 LYS cc_start: 0.8017 (pttm) cc_final: 0.7665 (tmtt) REVERT: D 268 ILE cc_start: 0.8283 (pt) cc_final: 0.7884 (mt) REVERT: E 254 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7914 (mt-10) REVERT: F 11 ARG cc_start: 0.8343 (ptt180) cc_final: 0.8003 (ptt180) REVERT: F 122 LYS cc_start: 0.7895 (tptt) cc_final: 0.7530 (tptp) REVERT: F 210 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7738 (ttm170) REVERT: F 294 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (t) REVERT: G 177 MET cc_start: 0.5114 (ttt) cc_final: 0.4778 (tmm) REVERT: G 552 ASP cc_start: 0.7691 (m-30) cc_final: 0.7435 (m-30) REVERT: I 92 LEU cc_start: 0.3369 (OUTLIER) cc_final: 0.3061 (pp) REVERT: I 257 ASP cc_start: 0.6784 (p0) cc_final: 0.6052 (p0) REVERT: I 292 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7319 (ptp90) REVERT: I 294 LEU cc_start: 0.7617 (mt) cc_final: 0.6664 (mt) REVERT: I 365 TYR cc_start: 0.7627 (m-80) cc_final: 0.7344 (m-80) REVERT: J 2 PHE cc_start: 0.8209 (t80) cc_final: 0.7966 (t80) REVERT: J 261 PHE cc_start: 0.3452 (t80) cc_final: 0.2605 (m-10) outliers start: 88 outliers final: 42 residues processed: 382 average time/residue: 0.3873 time to fit residues: 238.3371 Evaluate side-chains 309 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 265 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 323 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 0.0970 chunk 338 optimal weight: 10.0000 chunk 278 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 251 optimal weight: 20.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS J 46 HIS J 66 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29728 Z= 0.180 Angle : 0.717 15.271 40627 Z= 0.370 Chirality : 0.044 0.211 4489 Planarity : 0.005 0.080 4986 Dihedral : 15.248 179.624 4655 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.84 % Favored : 83.46 % Rotamer: Outliers : 3.43 % Allowed : 14.07 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 5.45 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.13), residues: 3391 helix: -1.21 (0.16), residues: 950 sheet: -1.33 (0.23), residues: 500 loop : -3.47 (0.12), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 24 HIS 0.006 0.001 HIS D 84 PHE 0.016 0.001 PHE I 238 TYR 0.031 0.001 TYR G 622 ARG 0.005 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 296 time to evaluate : 3.152 Fit side-chains revert: symmetry clash REVERT: A 157 THR cc_start: 0.8786 (m) cc_final: 0.8387 (p) REVERT: B 117 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8024 (mt-10) REVERT: B 195 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8232 (mtmm) REVERT: C 96 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 99 GLN cc_start: 0.8099 (mt0) cc_final: 0.7394 (mp10) REVERT: C 107 LYS cc_start: 0.7714 (tptt) cc_final: 0.7209 (tttt) REVERT: C 292 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 69 ASN cc_start: 0.8133 (p0) cc_final: 0.7880 (p0) REVERT: D 107 LYS cc_start: 0.8104 (pttm) cc_final: 0.7600 (tmtt) REVERT: D 268 ILE cc_start: 0.8231 (pt) cc_final: 0.7819 (mt) REVERT: F 122 LYS cc_start: 0.7861 (tptt) cc_final: 0.7498 (tptp) REVERT: F 210 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7744 (ttm170) REVERT: F 280 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: F 294 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (t) REVERT: G 71 TRP cc_start: 0.4080 (OUTLIER) cc_final: 0.1926 (t60) REVERT: G 552 ASP cc_start: 0.7601 (m-30) cc_final: 0.7329 (m-30) REVERT: I 75 PHE cc_start: 0.4671 (OUTLIER) cc_final: 0.4384 (t80) REVERT: I 294 LEU cc_start: 0.7536 (mt) cc_final: 0.6601 (mt) REVERT: I 365 TYR cc_start: 0.7757 (m-80) cc_final: 0.7431 (m-80) REVERT: J 2 PHE cc_start: 0.7948 (t80) cc_final: 0.7630 (t80) REVERT: J 244 PHE cc_start: 0.5209 (OUTLIER) cc_final: 0.4462 (m-10) REVERT: J 261 PHE cc_start: 0.3526 (t80) cc_final: 0.2671 (m-10) REVERT: J 296 HIS cc_start: 0.6088 (m-70) cc_final: 0.5564 (m-70) REVERT: J 323 MET cc_start: 0.4822 (OUTLIER) cc_final: 0.4561 (mmp) REVERT: J 385 PHE cc_start: 0.2773 (OUTLIER) cc_final: 0.2435 (t80) outliers start: 104 outliers final: 59 residues processed: 372 average time/residue: 0.3712 time to fit residues: 225.7236 Evaluate side-chains 324 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 chunk 332 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN E 42 GLN F 311 GLN G 85 HIS I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29728 Z= 0.310 Angle : 0.767 12.718 40627 Z= 0.396 Chirality : 0.047 0.226 4489 Planarity : 0.005 0.080 4986 Dihedral : 15.212 174.767 4652 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.87 % Favored : 83.37 % Rotamer: Outliers : 4.15 % Allowed : 15.45 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 5.45 % Twisted General : 0.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.13), residues: 3391 helix: -1.20 (0.16), residues: 954 sheet: -1.17 (0.23), residues: 486 loop : -3.41 (0.12), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 24 HIS 0.007 0.001 HIS J 252 PHE 0.020 0.002 PHE D 89 TYR 0.027 0.002 TYR G 622 ARG 0.006 0.001 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 265 time to evaluate : 3.252 Fit side-chains REVERT: B 102 LYS cc_start: 0.7486 (mtmt) cc_final: 0.6910 (mtpt) REVERT: B 195 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8223 (mtmm) REVERT: B 334 MET cc_start: 0.8487 (mmm) cc_final: 0.8273 (mmm) REVERT: C 99 GLN cc_start: 0.8118 (mt0) cc_final: 0.7381 (mp10) REVERT: C 107 LYS cc_start: 0.7860 (tptt) cc_final: 0.7306 (tttt) REVERT: C 210 ARG cc_start: 0.7819 (ptm160) cc_final: 0.6956 (ptp90) REVERT: C 292 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 69 ASN cc_start: 0.8102 (p0) cc_final: 0.7880 (p0) REVERT: D 107 LYS cc_start: 0.8088 (pttm) cc_final: 0.7541 (tmtt) REVERT: D 268 ILE cc_start: 0.8391 (pt) cc_final: 0.8027 (mt) REVERT: F 122 LYS cc_start: 0.7881 (tptt) cc_final: 0.7524 (tptp) REVERT: F 210 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7705 (ttm170) REVERT: F 226 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8269 (m) REVERT: F 280 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: F 294 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8327 (t) REVERT: G 71 TRP cc_start: 0.4312 (OUTLIER) cc_final: 0.1944 (t60) REVERT: G 583 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7724 (tp) REVERT: I 75 PHE cc_start: 0.4846 (OUTLIER) cc_final: 0.4535 (t80) REVERT: I 243 PHE cc_start: 0.7373 (t80) cc_final: 0.7043 (t80) REVERT: I 365 TYR cc_start: 0.7615 (m-80) cc_final: 0.7414 (m-80) REVERT: J 2 PHE cc_start: 0.8027 (t80) cc_final: 0.7685 (t80) REVERT: J 240 PHE cc_start: 0.5955 (t80) cc_final: 0.5050 (t80) REVERT: J 244 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.4004 (m-10) REVERT: J 261 PHE cc_start: 0.3536 (t80) cc_final: 0.2646 (m-10) REVERT: J 366 LEU cc_start: 0.3891 (OUTLIER) cc_final: 0.3363 (mp) REVERT: J 385 PHE cc_start: 0.3247 (OUTLIER) cc_final: 0.2929 (t80) outliers start: 126 outliers final: 87 residues processed: 357 average time/residue: 0.3592 time to fit residues: 211.6527 Evaluate side-chains 341 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 245 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 582 SER Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 30.0000 chunk 229 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS B 311 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN E 42 GLN E 214 HIS F 311 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 29728 Z= 0.541 Angle : 0.891 13.509 40627 Z= 0.460 Chirality : 0.052 0.305 4489 Planarity : 0.007 0.079 4986 Dihedral : 15.473 172.169 4652 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.71 % Allowed : 17.69 % Favored : 81.60 % Rotamer: Outliers : 5.30 % Allowed : 15.98 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 1.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.13), residues: 3391 helix: -1.62 (0.15), residues: 982 sheet: -1.29 (0.23), residues: 507 loop : -3.53 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 24 HIS 0.009 0.002 HIS J 252 PHE 0.034 0.003 PHE E 89 TYR 0.026 0.002 TYR G 622 ARG 0.007 0.001 ARG F 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 256 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7677 (mtm110) REVERT: A 334 MET cc_start: 0.7574 (mpp) cc_final: 0.7338 (mpp) REVERT: B 102 LYS cc_start: 0.7606 (mtmt) cc_final: 0.6954 (mtpt) REVERT: B 195 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8212 (mtmm) REVERT: C 48 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7799 (tt) REVERT: C 107 LYS cc_start: 0.7896 (tptt) cc_final: 0.7309 (tttt) REVERT: C 210 ARG cc_start: 0.7901 (ptm160) cc_final: 0.6969 (ptp90) REVERT: C 252 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7757 (t0) REVERT: C 292 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 107 LYS cc_start: 0.8114 (pttm) cc_final: 0.7558 (tmtt) REVERT: D 338 MET cc_start: 0.8722 (mmp) cc_final: 0.8173 (tpp) REVERT: D 347 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8810 (p90) REVERT: F 122 LYS cc_start: 0.7948 (tptt) cc_final: 0.7589 (tptp) REVERT: F 210 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7615 (ttm170) REVERT: F 226 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8301 (m) REVERT: F 229 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: F 294 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (t) REVERT: G 71 TRP cc_start: 0.4716 (OUTLIER) cc_final: 0.2065 (t60) REVERT: G 406 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8098 (m) REVERT: G 436 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6161 (pt0) REVERT: H 18 GLU cc_start: 0.6974 (mp0) cc_final: 0.6695 (mt-10) REVERT: H 25 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6782 (tt) REVERT: H 186 LEU cc_start: 0.5767 (tp) cc_final: 0.5502 (mt) REVERT: I 75 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4744 (t80) REVERT: I 195 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5413 (tt0) REVERT: I 247 TRP cc_start: 0.6086 (OUTLIER) cc_final: 0.4066 (t-100) REVERT: I 272 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6208 (tm-30) REVERT: I 294 LEU cc_start: 0.7867 (mt) cc_final: 0.7467 (mt) REVERT: J 2 PHE cc_start: 0.8261 (t80) cc_final: 0.8000 (t80) REVERT: J 244 PHE cc_start: 0.5124 (OUTLIER) cc_final: 0.4383 (m-10) REVERT: J 261 PHE cc_start: 0.3633 (t80) cc_final: 0.2594 (m-10) REVERT: J 366 LEU cc_start: 0.3923 (OUTLIER) cc_final: 0.3403 (mp) REVERT: J 385 PHE cc_start: 0.3069 (OUTLIER) cc_final: 0.2842 (t80) outliers start: 161 outliers final: 106 residues processed: 382 average time/residue: 0.3448 time to fit residues: 218.8913 Evaluate side-chains 365 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 241 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 490 HIS Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 8.9990 chunk 299 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 332 optimal weight: 20.0000 chunk 276 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN F 311 GLN I 135 ASN I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29728 Z= 0.201 Angle : 0.722 12.961 40627 Z= 0.371 Chirality : 0.045 0.224 4489 Planarity : 0.005 0.079 4986 Dihedral : 15.049 178.891 4650 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.31 % Favored : 84.08 % Rotamer: Outliers : 4.05 % Allowed : 17.76 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.14), residues: 3391 helix: -1.13 (0.17), residues: 959 sheet: -1.12 (0.23), residues: 509 loop : -3.33 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 24 HIS 0.006 0.001 HIS B 84 PHE 0.020 0.001 PHE I 238 TYR 0.026 0.001 TYR G 622 ARG 0.004 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 273 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8783 (m) cc_final: 0.8310 (p) REVERT: A 270 THR cc_start: 0.8583 (m) cc_final: 0.8179 (p) REVERT: A 331 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (mt) REVERT: B 195 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8166 (mtmm) REVERT: C 107 LYS cc_start: 0.7895 (tptt) cc_final: 0.7298 (tttt) REVERT: C 210 ARG cc_start: 0.7835 (ptm160) cc_final: 0.6912 (ptp90) REVERT: C 252 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7728 (t0) REVERT: D 107 LYS cc_start: 0.8033 (pttm) cc_final: 0.7534 (tttm) REVERT: D 171 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8302 (mp) REVERT: F 122 LYS cc_start: 0.7873 (tptt) cc_final: 0.7520 (tptp) REVERT: F 210 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7570 (ttm170) REVERT: F 226 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8223 (m) REVERT: F 280 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: F 294 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8233 (t) REVERT: G 436 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: H 18 GLU cc_start: 0.6802 (mp0) cc_final: 0.6551 (mt-10) REVERT: H 108 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7967 (t70) REVERT: I 1 MET cc_start: 0.0558 (ttt) cc_final: -0.0237 (tpp) REVERT: I 195 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5116 (tt0) REVERT: I 247 TRP cc_start: 0.6011 (OUTLIER) cc_final: 0.3633 (t-100) REVERT: J 2 PHE cc_start: 0.8241 (t80) cc_final: 0.7808 (t80) REVERT: J 244 PHE cc_start: 0.4872 (OUTLIER) cc_final: 0.3974 (m-10) REVERT: J 385 PHE cc_start: 0.3090 (OUTLIER) cc_final: 0.2812 (t80) outliers start: 123 outliers final: 84 residues processed: 363 average time/residue: 0.3967 time to fit residues: 237.5055 Evaluate side-chains 345 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 249 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 280 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 GLN I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 29728 Z= 0.411 Angle : 0.816 12.614 40627 Z= 0.419 Chirality : 0.049 0.258 4489 Planarity : 0.006 0.078 4986 Dihedral : 15.123 173.692 4650 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.68 % Allowed : 17.63 % Favored : 81.69 % Rotamer: Outliers : 4.94 % Allowed : 17.89 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.14), residues: 3391 helix: -1.38 (0.16), residues: 969 sheet: -1.20 (0.23), residues: 525 loop : -3.39 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 24 HIS 0.008 0.001 HIS D 84 PHE 0.024 0.002 PHE E 89 TYR 0.026 0.002 TYR G 622 ARG 0.006 0.001 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 256 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7552 (mtm110) REVERT: B 102 LYS cc_start: 0.7547 (mtmt) cc_final: 0.6905 (mtpt) REVERT: B 195 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8150 (mtmm) REVERT: C 48 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7761 (tt) REVERT: C 107 LYS cc_start: 0.7931 (tptt) cc_final: 0.7307 (tttt) REVERT: C 210 ARG cc_start: 0.7906 (ptm160) cc_final: 0.6946 (ptp90) REVERT: C 252 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7775 (t0) REVERT: C 292 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7783 (mm-30) REVERT: D 107 LYS cc_start: 0.8060 (pttm) cc_final: 0.7554 (tttm) REVERT: D 171 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8231 (mp) REVERT: D 338 MET cc_start: 0.8715 (mmp) cc_final: 0.8174 (tpp) REVERT: D 347 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8775 (p90) REVERT: F 122 LYS cc_start: 0.7895 (tptt) cc_final: 0.7541 (tptp) REVERT: F 210 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7635 (ttm170) REVERT: F 226 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8301 (m) REVERT: F 280 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: F 294 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8477 (t) REVERT: G 71 TRP cc_start: 0.4466 (OUTLIER) cc_final: 0.1809 (t60) REVERT: G 119 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5167 (p90) REVERT: G 406 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8089 (m) REVERT: G 436 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6067 (pt0) REVERT: G 546 SER cc_start: 0.7413 (m) cc_final: 0.6540 (t) REVERT: H 18 GLU cc_start: 0.6830 (mp0) cc_final: 0.6563 (mt-10) REVERT: I 195 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5347 (tt0) REVERT: I 247 TRP cc_start: 0.6093 (OUTLIER) cc_final: 0.3953 (t-100) REVERT: I 272 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: J 2 PHE cc_start: 0.8228 (t80) cc_final: 0.7987 (t80) REVERT: J 244 PHE cc_start: 0.5091 (OUTLIER) cc_final: 0.4280 (m-10) REVERT: J 366 LEU cc_start: 0.3906 (OUTLIER) cc_final: 0.3382 (mp) outliers start: 150 outliers final: 108 residues processed: 369 average time/residue: 0.3900 time to fit residues: 236.8451 Evaluate side-chains 377 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 252 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 490 HIS Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 366 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 0.0270 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 210 optimal weight: 0.0470 chunk 225 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN G 131 ASN I 123 HIS I 295 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29728 Z= 0.172 Angle : 0.705 12.811 40627 Z= 0.361 Chirality : 0.044 0.232 4489 Planarity : 0.005 0.078 4986 Dihedral : 14.803 179.261 4648 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.10 % Favored : 84.37 % Rotamer: Outliers : 3.92 % Allowed : 18.98 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.14), residues: 3391 helix: -0.99 (0.17), residues: 948 sheet: -1.05 (0.23), residues: 517 loop : -3.24 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 24 HIS 0.007 0.001 HIS I 123 PHE 0.021 0.001 PHE I 238 TYR 0.026 0.001 TYR G 622 ARG 0.006 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 292 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8100 (mtmm) REVERT: C 107 LYS cc_start: 0.7892 (tptt) cc_final: 0.7278 (ttpt) REVERT: C 210 ARG cc_start: 0.7878 (ptm160) cc_final: 0.6888 (ptp90) REVERT: C 252 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7765 (t0) REVERT: D 107 LYS cc_start: 0.8062 (pttm) cc_final: 0.7602 (tttm) REVERT: D 347 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8520 (p90) REVERT: F 122 LYS cc_start: 0.7784 (tptt) cc_final: 0.7421 (tptp) REVERT: F 226 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (m) REVERT: F 230 LYS cc_start: 0.6784 (pttp) cc_final: 0.5308 (mmmt) REVERT: F 280 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6673 (tp30) REVERT: F 294 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8226 (t) REVERT: G 436 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6090 (pt0) REVERT: G 546 SER cc_start: 0.7374 (m) cc_final: 0.6584 (t) REVERT: G 552 ASP cc_start: 0.7683 (m-30) cc_final: 0.7336 (m-30) REVERT: H 18 GLU cc_start: 0.6810 (mp0) cc_final: 0.6555 (mt-10) REVERT: I 1 MET cc_start: 0.0304 (ttt) cc_final: -0.0155 (tpp) REVERT: I 195 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.5046 (tt0) REVERT: I 243 PHE cc_start: 0.7397 (t80) cc_final: 0.7058 (t80) REVERT: J 2 PHE cc_start: 0.8135 (t80) cc_final: 0.7757 (t80) REVERT: J 244 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4122 (m-10) REVERT: J 281 ARG cc_start: 0.5577 (ttp-170) cc_final: 0.2436 (mtt-85) REVERT: J 323 MET cc_start: 0.3601 (mmt) cc_final: 0.0611 (mtp) REVERT: J 342 MET cc_start: 0.3653 (mmp) cc_final: 0.3320 (mmt) REVERT: J 366 LEU cc_start: 0.3738 (OUTLIER) cc_final: 0.3305 (mp) REVERT: J 385 PHE cc_start: 0.2807 (OUTLIER) cc_final: 0.2555 (t80) outliers start: 119 outliers final: 82 residues processed: 376 average time/residue: 0.3826 time to fit residues: 233.8547 Evaluate side-chains 351 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 259 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 490 HIS Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 289 optimal weight: 30.0000 chunk 308 optimal weight: 0.1980 chunk 185 optimal weight: 0.0050 chunk 134 optimal weight: 0.6980 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 279 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 29728 Z= 0.159 Angle : 0.692 11.746 40627 Z= 0.354 Chirality : 0.043 0.235 4489 Planarity : 0.005 0.077 4986 Dihedral : 14.632 179.396 4648 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.25 % Favored : 84.19 % Rotamer: Outliers : 3.10 % Allowed : 19.80 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 3391 helix: -0.74 (0.17), residues: 947 sheet: -0.92 (0.23), residues: 519 loop : -3.14 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 24 HIS 0.007 0.001 HIS I 237 PHE 0.025 0.001 PHE I 238 TYR 0.026 0.001 TYR G 622 ARG 0.007 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 292 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8747 (m) cc_final: 0.8288 (p) REVERT: B 195 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8147 (mtmm) REVERT: C 96 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 107 LYS cc_start: 0.7914 (tptt) cc_final: 0.7289 (tttt) REVERT: C 210 ARG cc_start: 0.7884 (ptm160) cc_final: 0.6929 (ptp90) REVERT: C 252 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7775 (t0) REVERT: C 292 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 107 LYS cc_start: 0.8022 (pttm) cc_final: 0.7585 (tmtt) REVERT: E 348 GLN cc_start: 0.7685 (pt0) cc_final: 0.7380 (pp30) REVERT: F 122 LYS cc_start: 0.7699 (tptt) cc_final: 0.7312 (tptp) REVERT: F 230 LYS cc_start: 0.6646 (pttp) cc_final: 0.5130 (mmmt) REVERT: F 280 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: F 294 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8151 (t) REVERT: G 436 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6018 (pt0) REVERT: G 546 SER cc_start: 0.7405 (m) cc_final: 0.6102 (t) REVERT: G 552 ASP cc_start: 0.7525 (m-30) cc_final: 0.7307 (m-30) REVERT: H 6 LYS cc_start: 0.6367 (mttm) cc_final: 0.6159 (mmtp) REVERT: H 88 ASN cc_start: 0.7638 (p0) cc_final: 0.7195 (p0) REVERT: I 1 MET cc_start: 0.0342 (ttt) cc_final: -0.0094 (tpp) REVERT: I 195 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5000 (tt0) REVERT: I 243 PHE cc_start: 0.7392 (t80) cc_final: 0.7152 (t80) REVERT: I 295 GLN cc_start: 0.6540 (pt0) cc_final: 0.5652 (tp40) REVERT: I 324 ASN cc_start: 0.7163 (t0) cc_final: 0.6918 (t0) REVERT: J 228 MET cc_start: 0.7424 (mtm) cc_final: 0.6622 (mmt) REVERT: J 244 PHE cc_start: 0.5155 (OUTLIER) cc_final: 0.4399 (m-10) REVERT: J 261 PHE cc_start: 0.4548 (t80) cc_final: 0.3294 (m-10) REVERT: J 281 ARG cc_start: 0.5600 (ttp-170) cc_final: 0.2527 (mtt-85) REVERT: J 323 MET cc_start: 0.3819 (mmt) cc_final: 0.0962 (mtp) REVERT: J 342 MET cc_start: 0.3571 (mmp) cc_final: 0.3260 (mmt) REVERT: J 366 LEU cc_start: 0.3813 (OUTLIER) cc_final: 0.3285 (mp) REVERT: J 385 PHE cc_start: 0.2870 (OUTLIER) cc_final: 0.2596 (t80) outliers start: 94 outliers final: 64 residues processed: 355 average time/residue: 0.3671 time to fit residues: 213.8172 Evaluate side-chains 330 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 258 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 202 ASN Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 10.0000 chunk 326 optimal weight: 0.5980 chunk 199 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 315 optimal weight: 2.9990 chunk 272 optimal weight: 20.0000 chunk 28 optimal weight: 0.0970 chunk 210 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN G 222 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS ** J 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 29728 Z= 0.159 Angle : 0.685 12.656 40627 Z= 0.349 Chirality : 0.043 0.253 4489 Planarity : 0.005 0.084 4986 Dihedral : 14.516 179.778 4647 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.04 % Favored : 84.43 % Rotamer: Outliers : 2.70 % Allowed : 20.26 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 3391 helix: -0.63 (0.17), residues: 952 sheet: -0.87 (0.23), residues: 519 loop : -3.10 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 24 HIS 0.023 0.001 HIS I 123 PHE 0.023 0.001 PHE I 238 TYR 0.024 0.001 TYR G 622 ARG 0.010 0.000 ARG I 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 286 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8197 (mtmm) REVERT: C 107 LYS cc_start: 0.7961 (tptt) cc_final: 0.7321 (tttt) REVERT: C 210 ARG cc_start: 0.7856 (ptm160) cc_final: 0.6934 (ptp90) REVERT: C 252 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7806 (t0) REVERT: C 292 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 107 LYS cc_start: 0.8028 (pttm) cc_final: 0.7573 (tmtt) REVERT: E 348 GLN cc_start: 0.7651 (pt0) cc_final: 0.7381 (pp30) REVERT: F 122 LYS cc_start: 0.7671 (tptt) cc_final: 0.7280 (tptp) REVERT: F 294 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8061 (t) REVERT: G 436 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5949 (pt0) REVERT: G 546 SER cc_start: 0.7368 (m) cc_final: 0.6026 (t) REVERT: G 552 ASP cc_start: 0.7544 (m-30) cc_final: 0.7340 (m-30) REVERT: H 88 ASN cc_start: 0.7642 (p0) cc_final: 0.7142 (p0) REVERT: I 1 MET cc_start: 0.0240 (ttt) cc_final: -0.0060 (tpp) REVERT: I 195 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.4962 (tt0) REVERT: I 238 PHE cc_start: 0.5104 (p90) cc_final: 0.4648 (p90) REVERT: I 295 GLN cc_start: 0.6646 (pt0) cc_final: 0.5691 (tp40) REVERT: I 324 ASN cc_start: 0.7195 (t0) cc_final: 0.6991 (t0) REVERT: J 281 ARG cc_start: 0.5516 (ttp-170) cc_final: 0.2516 (mtt-85) REVERT: J 323 MET cc_start: 0.3685 (mmt) cc_final: 0.0872 (mtp) REVERT: J 342 MET cc_start: 0.3548 (mmp) cc_final: 0.3237 (mmt) REVERT: J 366 LEU cc_start: 0.3810 (OUTLIER) cc_final: 0.3292 (mp) REVERT: J 385 PHE cc_start: 0.2862 (OUTLIER) cc_final: 0.2532 (t80) outliers start: 82 outliers final: 60 residues processed: 342 average time/residue: 0.3662 time to fit residues: 206.8597 Evaluate side-chains 324 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 0.0040 chunk 273 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 280 optimal weight: 9.9990 chunk 34 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 overall best weight: 0.7208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** 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 = 0.3986 r_free = 0.3986 target = 0.170427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135839 restraints weight = 43528.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133550 restraints weight = 58422.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135342 restraints weight = 53026.070| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29728 Z= 0.159 Angle : 0.686 11.771 40627 Z= 0.350 Chirality : 0.043 0.246 4489 Planarity : 0.005 0.081 4986 Dihedral : 14.426 179.247 4647 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.28 % Favored : 84.25 % Rotamer: Outliers : 2.57 % Allowed : 20.72 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.14), residues: 3391 helix: -0.54 (0.17), residues: 958 sheet: -0.79 (0.23), residues: 519 loop : -3.08 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 24 HIS 0.017 0.001 HIS I 123 PHE 0.023 0.001 PHE I 238 TYR 0.025 0.001 TYR G 622 ARG 0.004 0.000 ARG J 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5291.51 seconds wall clock time: 97 minutes 25.65 seconds (5845.65 seconds total)