Starting phenix.real_space_refine on Thu Mar 21 00:48:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/03_2024/6pif_20349.pdb" } resolution = 3.4 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 18194 2.51 5 N 5003 2.21 5 O 5556 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 ARG 178": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 314": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 145": "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 ARG 584": "NH1" <-> "NH2" Residue "G GLU 592": "OE1" <-> "OE2" Residue "G GLU 606": "OE1" <-> "OE2" Residue "G ARG 628": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 36": "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 ARG 168": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 281": "NH1" <-> "NH2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I GLU 344": "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 35": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 258": "OE1" <-> "OE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J GLU 291": "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" Residue "J GLU 384": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28954 Number of models: 1 Model: "" Number of chains: 11 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: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4093 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 1 Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2909 Classifications: {'peptide': 355} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 332} Chain breaks: 3 Chain: "J" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2982 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 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} Time building chain proxies: 15.31, per 1000 atoms: 0.53 Number of scatterers: 28954 At special positions: 0 Unit cell: (133, 164.35, 184.3, 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 5556 8.00 N 5003 7.00 C 18194 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: 11.71 Conformation dependent library (CDL) restraints added in 5.1 seconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 38 sheets defined 26.0% alpha, 13.0% beta 6 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.535A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.591A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.903A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.661A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.889A 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 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.946A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 4.007A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.873A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.675A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.973A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.712A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.569A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.634A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.776A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.932A pdb=" N SER C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.898A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.615A 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 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.686A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.803A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.842A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.897A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.708A pdb=" N GLN D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 319 removed outlier: 3.670A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 344 removed outlier: 3.504A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.846A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.519A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.648A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.003A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.906A pdb=" N ASN E 186 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP E 187 " --> pdb=" O ASN E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.600A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.700A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 Processing helix chain 'F' and resid 125 through 135 removed outlier: 4.068A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.913A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.021A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.682A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 344 removed outlier: 3.852A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.050A pdb=" N PHE G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.516A pdb=" N VAL G 44 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 160 through 167 removed outlier: 3.501A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'G' and resid 219 through 228 removed outlier: 3.733A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.538A pdb=" N MET G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.829A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 499 removed outlier: 3.684A pdb=" N VAL G 497 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 removed outlier: 3.713A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 558 removed outlier: 3.649A pdb=" N LEU G 553 " --> pdb=" O ASN G 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.822A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.693A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.242A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU I 35 " --> pdb=" O HIS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 82 removed outlier: 3.695A pdb=" N THR I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 218 through 228 removed outlier: 3.693A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 246 through 248 No H-bonds generated for 'chain 'I' and resid 246 through 248' Processing helix chain 'I' and resid 249 through 265 removed outlier: 3.969A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 4.250A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 337 through 345 Processing helix chain 'I' and resid 369 through 379 Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.628A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 43 Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.723A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.622A pdb=" N GLY J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 207 " --> pdb=" O TRP J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.607A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.513A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE J 261 " --> pdb=" O ASP J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 310 removed outlier: 3.657A pdb=" N LEU J 303 " --> pdb=" O ILE J 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 310 " --> pdb=" O TYR J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 333 removed outlier: 3.739A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 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: 3.597A pdb=" N SER A 88 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 166 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 41 removed outlier: 3.500A pdb=" N VAL A 73 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 removed outlier: 4.081A pdb=" N GLU A 254 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.733A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.830A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.795A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB6, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB7, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.781A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'E' and resid 270 through 272 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: 3.891A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.394A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'G' and resid 201 through 204 removed outlier: 3.726A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.560A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD4, first strand: chain 'G' and resid 457 through 458 Processing sheet with id=AD5, first strand: chain 'G' and resid 539 through 542 Processing sheet with id=AD6, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.664A pdb=" N VAL H 90 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.599A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.585A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 322 through 324 748 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5575 1.34 - 1.46: 7880 1.46 - 1.58: 16036 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29814 Sorted by residual: bond pdb=" CD GLU D 127 " pdb=" OE1 GLU D 127 " ideal model delta sigma weight residual 1.249 1.415 -0.166 1.90e-02 2.77e+03 7.61e+01 bond pdb=" CD GLU D 127 " pdb=" OE2 GLU D 127 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" N GLY D 285 " pdb=" CA GLY D 285 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.497 -0.037 8.60e-03 1.35e+04 1.81e+01 bond pdb=" N ILE J 347 " pdb=" CA ILE J 347 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.80e+01 ... (remaining 29809 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.73: 813 104.73 - 112.18: 13306 112.18 - 119.63: 14352 119.63 - 127.09: 11731 127.09 - 134.54: 540 Bond angle restraints: 40742 Sorted by residual: angle pdb=" N PRO I 86 " pdb=" CA PRO I 86 " pdb=" CB PRO I 86 " ideal model delta sigma weight residual 103.08 97.36 5.72 9.70e-01 1.06e+00 3.48e+01 angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 97.27 5.98 1.05e+00 9.07e-01 3.24e+01 angle pdb=" C CYS I 131 " pdb=" CA CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.08e+01 angle pdb=" CA GLY H 177 " pdb=" C GLY H 177 " pdb=" O GLY H 177 " ideal model delta sigma weight residual 122.33 117.88 4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" N PRO D 276 " pdb=" CA PRO D 276 " pdb=" CB PRO D 276 " ideal model delta sigma weight residual 103.25 97.79 5.46 1.05e+00 9.07e-01 2.70e+01 ... (remaining 40737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17266 35.78 - 71.56: 509 71.56 - 107.34: 42 107.34 - 143.12: 4 143.12 - 178.90: 3 Dihedral angle restraints: 17824 sinusoidal: 7710 harmonic: 10114 Sorted by residual: dihedral pdb=" CA LYS G 49 " pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta harmonic sigma weight residual 180.00 45.09 134.91 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N ASP G 58 " pdb=" CA ASP G 58 " ideal model delta harmonic sigma weight residual 180.00 68.17 111.83 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA ASP G 58 " pdb=" C ASP G 58 " pdb=" N ARG G 59 " pdb=" CA ARG G 59 " ideal model delta harmonic sigma weight residual -180.00 -73.00 -107.00 0 5.00e+00 4.00e-02 4.58e+02 ... (remaining 17821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 1611 0.115 - 0.172: 671 0.172 - 0.230: 148 0.230 - 0.287: 9 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1' U 1 21 " pdb=" O4' U 1 21 " pdb=" C2' U 1 21 " pdb=" N1 U 1 21 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA GLU I 85 " pdb=" N GLU I 85 " pdb=" C GLU I 85 " pdb=" CB GLU I 85 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA TYR I 140 " pdb=" N TYR I 140 " pdb=" C TYR I 140 " pdb=" CB TYR I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4500 not shown) Planarity restraints: 5002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 127 " -0.064 2.00e-02 2.50e+03 1.20e-01 1.44e+02 pdb=" CD GLU D 127 " 0.208 2.00e-02 2.50e+03 pdb=" OE1 GLU D 127 " -0.069 2.00e-02 2.50e+03 pdb=" OE2 GLU D 127 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 403 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C SER G 403 " -0.043 2.00e-02 2.50e+03 pdb=" O SER G 403 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 404 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 7 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS I 7 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS I 7 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO I 8 " 0.013 2.00e-02 2.50e+03 ... (remaining 4999 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 34 1.99 - 2.71: 1053 2.71 - 3.44: 37508 3.44 - 4.17: 66348 4.17 - 4.90: 117979 Nonbonded interactions: 222922 Sorted by model distance: nonbonded pdb=" CG TYR H 5 " pdb=" CD1 ILE H 199 " model vdw 1.256 3.680 nonbonded pdb=" CE MET F 346 " pdb=" N1 U 1 35 " model vdw 1.271 3.540 nonbonded pdb=" CD1 ILE G 42 " pdb=" CB LEU G 56 " model vdw 1.282 3.860 nonbonded pdb=" O ASP G 48 " pdb=" ND2 ASN G 131 " model vdw 1.347 2.520 nonbonded pdb=" CE MET F 220 " pdb=" N7 G 1 41 " model vdw 1.376 3.540 ... (remaining 222917 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 232 or resid 236 through 351 or resid 361 throug \ h 393)) selection = (chain 'J' and (resid 1 through 162 or resid 195 through 351 or resid 361 throug \ h 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.020 Extract box with map and model: 7.390 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 77.660 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 0.166 29814 Z= 0.897 Angle : 1.740 9.218 40742 Z= 1.230 Chirality : 0.085 0.287 4503 Planarity : 0.004 0.120 5002 Dihedral : 17.072 178.905 11252 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 3.91 % Allowed : 14.76 % Favored : 81.32 % Rotamer: Outliers : 2.17 % Allowed : 6.20 % Favored : 91.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 6.06 % Twisted General : 2.55 % 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: -4.83 (0.11), residues: 3400 helix: -2.66 (0.14), residues: 880 sheet: -1.93 (0.21), residues: 477 loop : -4.02 (0.11), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 24 HIS 0.009 0.002 HIS E 299 PHE 0.019 0.002 PHE I 144 TYR 0.025 0.002 TYR I 101 ARG 0.018 0.001 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 643 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 42 GLN cc_start: 0.7782 (pt0) cc_final: 0.7581 (pt0) REVERT: A 293 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5839 (p0) REVERT: B 43 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: B 134 MET cc_start: 0.8398 (mtm) cc_final: 0.8003 (mtp) REVERT: B 333 ASP cc_start: 0.8388 (m-30) cc_final: 0.8150 (m-30) REVERT: C 210 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7435 (ptp90) REVERT: C 244 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8194 (ttm170) REVERT: C 324 LYS cc_start: 0.7295 (tppt) cc_final: 0.6639 (tptm) REVERT: D 71 HIS cc_start: 0.6693 (m-70) cc_final: 0.6329 (t-170) REVERT: D 120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 291 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7127 (ttp-170) REVERT: F 6 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (m-40) REVERT: F 71 HIS cc_start: 0.6126 (t-90) cc_final: 0.5684 (t-90) REVERT: F 88 SER cc_start: 0.7864 (t) cc_final: 0.7389 (p) REVERT: F 195 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7686 (ttmm) REVERT: F 210 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7325 (ttm-80) REVERT: F 263 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8105 (tptt) REVERT: F 308 SER cc_start: 0.8416 (m) cc_final: 0.7847 (t) REVERT: G 47 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6871 (t) REVERT: G 190 ASN cc_start: 0.7309 (t0) cc_final: 0.6925 (m110) REVERT: G 205 ASP cc_start: 0.7884 (p0) cc_final: 0.7615 (p0) REVERT: G 469 THR cc_start: 0.7726 (p) cc_final: 0.7351 (p) REVERT: G 613 PHE cc_start: 0.7354 (m-80) cc_final: 0.6851 (m-80) REVERT: H 77 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7318 (mt0) REVERT: H 81 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8369 (pp) REVERT: H 127 LEU cc_start: 0.6116 (mm) cc_final: 0.5639 (pp) REVERT: I 1 MET cc_start: 0.0525 (tpt) cc_final: 0.0163 (mmm) REVERT: I 57 THR cc_start: 0.5045 (m) cc_final: 0.4769 (p) REVERT: I 130 LEU cc_start: 0.2321 (OUTLIER) cc_final: 0.1984 (mm) REVERT: I 198 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5413 (t) REVERT: I 272 GLU cc_start: 0.7840 (pt0) cc_final: 0.7570 (mp0) REVERT: I 383 ASP cc_start: 0.7937 (p0) cc_final: 0.7729 (p0) REVERT: I 386 ASN cc_start: 0.8150 (t0) cc_final: 0.7949 (t0) REVERT: J 43 ASP cc_start: 0.7734 (m-30) cc_final: 0.7326 (m-30) REVERT: J 47 ASN cc_start: 0.7751 (p0) cc_final: 0.7530 (m-40) REVERT: J 217 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7294 (tttt) outliers start: 66 outliers final: 25 residues processed: 694 average time/residue: 0.4627 time to fit residues: 487.7641 Evaluate side-chains 357 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 324 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 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 117 GLU Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 276 PRO Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 533 PRO Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 174 ASN A 218 ASN B 135 ASN B 183 ASN B 311 GLN B 312 GLN B 315 HIS C 104 ASN C 174 ASN C 311 GLN D 110 GLN D 174 ASN D 183 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN F 183 ASN F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS F 349 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 196 ASN G 227 GLN G 384 ASN G 392 ASN G 444 GLN G 490 HIS ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS H 16 ASN H 88 ASN H 132 GLN I 80 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS I 265 HIS J 46 HIS J 95 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29814 Z= 0.253 Angle : 0.828 11.723 40742 Z= 0.432 Chirality : 0.048 0.282 4503 Planarity : 0.005 0.092 5002 Dihedral : 15.916 175.716 4722 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 1.09 % Allowed : 13.76 % Favored : 85.15 % Rotamer: Outliers : 3.35 % Allowed : 11.88 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 6.06 % Twisted General : 1.75 % 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: -3.86 (0.13), residues: 3400 helix: -1.38 (0.17), residues: 901 sheet: -1.06 (0.22), residues: 479 loop : -3.75 (0.11), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 24 HIS 0.010 0.001 HIS G 490 PHE 0.021 0.002 PHE G 433 TYR 0.025 0.002 TYR J 169 ARG 0.010 0.001 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 360 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8024 (tp40) cc_final: 0.7685 (tp-100) REVERT: A 229 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6199 (mt-10) REVERT: B 17 ASP cc_start: 0.8207 (p0) cc_final: 0.7730 (p0) REVERT: B 169 GLU cc_start: 0.7203 (tp30) cc_final: 0.6702 (pm20) REVERT: B 185 LYS cc_start: 0.5193 (pttm) cc_final: 0.4821 (mtmt) REVERT: C 252 ASP cc_start: 0.7810 (m-30) cc_final: 0.7466 (t0) REVERT: C 324 LYS cc_start: 0.7305 (tppt) cc_final: 0.6959 (mmtt) REVERT: D 71 HIS cc_start: 0.6772 (m-70) cc_final: 0.6362 (t-170) REVERT: D 210 ARG cc_start: 0.7701 (tpp-160) cc_final: 0.7499 (ttm110) REVERT: D 291 ARG cc_start: 0.7627 (ttt90) cc_final: 0.7150 (ttp-170) REVERT: E 210 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6952 (ttp80) REVERT: E 241 GLN cc_start: 0.5047 (OUTLIER) cc_final: 0.4818 (pm20) REVERT: F 88 SER cc_start: 0.8008 (t) cc_final: 0.7673 (p) REVERT: F 188 SER cc_start: 0.8992 (m) cc_final: 0.8534 (p) REVERT: F 210 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7165 (ttm170) REVERT: F 308 SER cc_start: 0.8445 (m) cc_final: 0.8164 (p) REVERT: G 19 LEU cc_start: 0.8221 (tp) cc_final: 0.7925 (tp) REVERT: G 23 PHE cc_start: 0.8010 (m-80) cc_final: 0.7703 (m-80) REVERT: G 190 ASN cc_start: 0.7634 (t0) cc_final: 0.7035 (m110) REVERT: G 469 THR cc_start: 0.7775 (p) cc_final: 0.7560 (p) REVERT: H 16 ASN cc_start: 0.8223 (t0) cc_final: 0.7916 (t0) REVERT: H 102 ARG cc_start: 0.6529 (ptp-170) cc_final: 0.6171 (ttt-90) REVERT: H 127 LEU cc_start: 0.5713 (mm) cc_final: 0.5449 (pp) REVERT: H 197 PRO cc_start: 0.8573 (Cg_endo) cc_final: 0.8060 (Cg_exo) REVERT: I 3 LEU cc_start: 0.5521 (tp) cc_final: 0.4358 (mt) REVERT: I 198 CYS cc_start: 0.5758 (OUTLIER) cc_final: 0.5406 (t) REVERT: I 217 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7102 (mttp) REVERT: I 239 SER cc_start: 0.4658 (m) cc_final: 0.4343 (t) REVERT: I 272 GLU cc_start: 0.7907 (pt0) cc_final: 0.7540 (mp0) REVERT: J 43 ASP cc_start: 0.7335 (m-30) cc_final: 0.6875 (m-30) REVERT: J 47 ASN cc_start: 0.8103 (p0) cc_final: 0.7512 (m-40) REVERT: J 108 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6538 (m) REVERT: J 367 PHE cc_start: 0.6239 (m-10) cc_final: 0.6037 (m-10) REVERT: J 375 LEU cc_start: 0.7319 (tp) cc_final: 0.6716 (tt) outliers start: 102 outliers final: 56 residues processed: 439 average time/residue: 0.4066 time to fit residues: 285.5481 Evaluate side-chains 337 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 278 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 186 ASN A 311 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 299 HIS ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 349 HIS F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 548 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS H 160 ASN I 31 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29814 Z= 0.328 Angle : 0.807 11.514 40742 Z= 0.422 Chirality : 0.048 0.275 4503 Planarity : 0.005 0.058 5002 Dihedral : 15.421 178.448 4672 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.82 % Allowed : 15.82 % Favored : 83.35 % Rotamer: Outliers : 4.07 % Allowed : 13.98 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.85 % Twisted General : 1.50 % 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: -3.58 (0.13), residues: 3400 helix: -1.06 (0.17), residues: 900 sheet: -0.87 (0.23), residues: 476 loop : -3.61 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 203 HIS 0.018 0.001 HIS H 73 PHE 0.023 0.002 PHE G 613 TYR 0.021 0.002 TYR G 543 ARG 0.007 0.001 ARG G 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 313 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8038 (tp40) cc_final: 0.7728 (tp-100) REVERT: A 307 PHE cc_start: 0.7979 (m-10) cc_final: 0.7552 (m-10) REVERT: B 23 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8638 (m) REVERT: B 96 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8033 (mt-10) REVERT: B 170 ASP cc_start: 0.8274 (t0) cc_final: 0.7580 (p0) REVERT: C 252 ASP cc_start: 0.7806 (m-30) cc_final: 0.7446 (t0) REVERT: C 280 GLU cc_start: 0.7492 (tt0) cc_final: 0.6981 (tp30) REVERT: D 71 HIS cc_start: 0.7029 (m-70) cc_final: 0.6556 (t-170) REVERT: D 291 ARG cc_start: 0.7566 (ttt90) cc_final: 0.7018 (ttp-170) REVERT: E 210 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6945 (ttp80) REVERT: E 252 ASP cc_start: 0.8405 (t0) cc_final: 0.7976 (t0) REVERT: F 37 ARG cc_start: 0.7258 (ttp80) cc_final: 0.7012 (mtp180) REVERT: F 88 SER cc_start: 0.8103 (t) cc_final: 0.7795 (m) REVERT: F 188 SER cc_start: 0.9008 (m) cc_final: 0.8559 (p) REVERT: F 210 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.6919 (ttm170) REVERT: F 218 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8322 (t0) REVERT: F 308 SER cc_start: 0.8487 (m) cc_final: 0.8193 (p) REVERT: G 19 LEU cc_start: 0.8281 (tp) cc_final: 0.7778 (tp) REVERT: G 23 PHE cc_start: 0.7929 (m-80) cc_final: 0.7656 (m-80) REVERT: G 231 ASP cc_start: 0.7414 (m-30) cc_final: 0.6917 (p0) REVERT: H 16 ASN cc_start: 0.8214 (t0) cc_final: 0.7842 (t0) REVERT: H 81 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8473 (pp) REVERT: H 88 ASN cc_start: 0.7252 (m-40) cc_final: 0.6700 (t0) REVERT: H 127 LEU cc_start: 0.5739 (mm) cc_final: 0.5502 (pp) REVERT: H 164 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6605 (mtp180) REVERT: H 181 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.3769 (p90) REVERT: H 190 GLU cc_start: 0.5896 (pt0) cc_final: 0.5634 (pt0) REVERT: I 3 LEU cc_start: 0.5795 (tp) cc_final: 0.4524 (mt) REVERT: I 198 CYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5334 (t) REVERT: I 217 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7210 (mttp) REVERT: I 272 GLU cc_start: 0.7898 (pt0) cc_final: 0.7564 (mp0) REVERT: I 326 LEU cc_start: 0.8198 (mt) cc_final: 0.7970 (mp) REVERT: J 43 ASP cc_start: 0.7285 (m-30) cc_final: 0.6922 (m-30) REVERT: J 47 ASN cc_start: 0.8226 (p0) cc_final: 0.7694 (m110) REVERT: J 163 CYS cc_start: 0.6345 (m) cc_final: 0.6092 (m) REVERT: J 242 GLN cc_start: 0.8241 (mm110) cc_final: 0.7292 (tm-30) outliers start: 124 outliers final: 75 residues processed: 413 average time/residue: 0.3843 time to fit residues: 256.4118 Evaluate side-chains 356 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 275 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 499 SER 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 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 8.9990 chunk 235 optimal weight: 0.0970 chunk 162 optimal weight: 0.0270 chunk 34 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 333 optimal weight: 30.0000 chunk 164 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29814 Z= 0.235 Angle : 0.745 11.021 40742 Z= 0.387 Chirality : 0.045 0.249 4503 Planarity : 0.005 0.055 5002 Dihedral : 15.100 176.939 4670 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.82 % Allowed : 14.62 % Favored : 84.56 % Rotamer: Outliers : 3.77 % Allowed : 15.45 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.64 % Twisted General : 1.01 % 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: -3.45 (0.13), residues: 3400 helix: -0.95 (0.17), residues: 930 sheet: -0.93 (0.23), residues: 498 loop : -3.55 (0.12), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 203 HIS 0.007 0.001 HIS B 84 PHE 0.016 0.001 PHE I 238 TYR 0.019 0.001 TYR I 390 ARG 0.009 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 301 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8136 (tp40) cc_final: 0.7859 (tp-100) REVERT: B 23 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 99 GLN cc_start: 0.8056 (pm20) cc_final: 0.7694 (pm20) REVERT: B 138 ASN cc_start: 0.8101 (p0) cc_final: 0.7616 (p0) REVERT: B 170 ASP cc_start: 0.7969 (t0) cc_final: 0.7747 (p0) REVERT: C 252 ASP cc_start: 0.7860 (m-30) cc_final: 0.7430 (t0) REVERT: C 280 GLU cc_start: 0.7314 (tt0) cc_final: 0.6923 (tp30) REVERT: D 71 HIS cc_start: 0.6981 (m-70) cc_final: 0.6581 (t-170) REVERT: D 291 ARG cc_start: 0.7572 (ttt90) cc_final: 0.7049 (ttp-170) REVERT: E 210 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6980 (ttp80) REVERT: E 252 ASP cc_start: 0.8382 (t0) cc_final: 0.7967 (t0) REVERT: E 333 ASP cc_start: 0.7948 (m-30) cc_final: 0.7561 (m-30) REVERT: F 88 SER cc_start: 0.8093 (t) cc_final: 0.7762 (m) REVERT: F 188 SER cc_start: 0.8921 (m) cc_final: 0.8483 (p) REVERT: F 210 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6901 (ttm170) REVERT: F 308 SER cc_start: 0.8343 (m) cc_final: 0.8093 (p) REVERT: G 19 LEU cc_start: 0.8320 (tp) cc_final: 0.7925 (tp) REVERT: G 23 PHE cc_start: 0.7967 (m-80) cc_final: 0.7436 (m-80) REVERT: G 231 ASP cc_start: 0.7137 (m-30) cc_final: 0.6866 (p0) REVERT: H 16 ASN cc_start: 0.8258 (t0) cc_final: 0.7912 (t0) REVERT: H 81 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8458 (pp) REVERT: H 88 ASN cc_start: 0.7218 (m-40) cc_final: 0.6700 (t0) REVERT: H 164 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6611 (mtp180) REVERT: I 110 ARG cc_start: 0.5553 (tpm170) cc_final: 0.4186 (tpm170) REVERT: I 198 CYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5405 (t) REVERT: I 217 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7231 (mttp) REVERT: I 272 GLU cc_start: 0.7888 (pt0) cc_final: 0.7576 (mp0) REVERT: I 326 LEU cc_start: 0.8188 (mt) cc_final: 0.7976 (mp) REVERT: J 43 ASP cc_start: 0.7382 (m-30) cc_final: 0.7030 (m-30) REVERT: J 47 ASN cc_start: 0.8371 (p0) cc_final: 0.7739 (m110) outliers start: 115 outliers final: 77 residues processed: 394 average time/residue: 0.3841 time to fit residues: 246.1300 Evaluate side-chains 351 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 270 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER 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 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 262 ASN Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 248 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN F 77 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 618 ASN G 626 GLN H 39 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS I 351 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29814 Z= 0.348 Angle : 0.789 13.265 40742 Z= 0.409 Chirality : 0.047 0.298 4503 Planarity : 0.005 0.056 5002 Dihedral : 14.986 178.983 4666 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.82 % Allowed : 16.24 % Favored : 82.94 % Rotamer: Outliers : 4.82 % Allowed : 15.49 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 1.07 % 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: -3.35 (0.13), residues: 3400 helix: -0.90 (0.17), residues: 926 sheet: -0.68 (0.23), residues: 500 loop : -3.52 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 203 HIS 0.007 0.001 HIS B 84 PHE 0.021 0.002 PHE G 613 TYR 0.032 0.002 TYR G 197 ARG 0.005 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 292 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8100 (tp40) cc_final: 0.7819 (tp-100) REVERT: A 307 PHE cc_start: 0.7892 (m-10) cc_final: 0.7543 (m-10) REVERT: B 23 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8620 (m) REVERT: B 99 GLN cc_start: 0.8188 (pm20) cc_final: 0.7863 (pm20) REVERT: B 138 ASN cc_start: 0.8197 (p0) cc_final: 0.7952 (p0) REVERT: B 170 ASP cc_start: 0.8084 (t0) cc_final: 0.7729 (p0) REVERT: C 252 ASP cc_start: 0.7832 (m-30) cc_final: 0.7433 (t0) REVERT: C 280 GLU cc_start: 0.7354 (tt0) cc_final: 0.6908 (tp30) REVERT: C 347 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: D 71 HIS cc_start: 0.7013 (m-70) cc_final: 0.6536 (t-170) REVERT: D 291 ARG cc_start: 0.7653 (ttt90) cc_final: 0.7014 (ttp-170) REVERT: E 210 ARG cc_start: 0.7275 (ttm170) cc_final: 0.6998 (ttp80) REVERT: E 252 ASP cc_start: 0.8451 (t0) cc_final: 0.8005 (t0) REVERT: E 333 ASP cc_start: 0.7961 (m-30) cc_final: 0.7573 (m-30) REVERT: F 88 SER cc_start: 0.8131 (t) cc_final: 0.7832 (m) REVERT: F 188 SER cc_start: 0.8988 (m) cc_final: 0.8538 (p) REVERT: F 210 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7267 (ttm170) REVERT: G 19 LEU cc_start: 0.8238 (tp) cc_final: 0.7893 (tp) REVERT: G 23 PHE cc_start: 0.7964 (m-80) cc_final: 0.7496 (m-80) REVERT: G 515 ASP cc_start: 0.7582 (t70) cc_final: 0.7354 (t70) REVERT: G 622 TYR cc_start: 0.7923 (p90) cc_final: 0.7636 (p90) REVERT: H 16 ASN cc_start: 0.8282 (t0) cc_final: 0.8016 (t0) REVERT: H 40 ILE cc_start: 0.8074 (mm) cc_final: 0.7809 (mt) REVERT: H 88 ASN cc_start: 0.7273 (m-40) cc_final: 0.6690 (t0) REVERT: H 105 GLN cc_start: 0.8629 (tt0) cc_final: 0.8371 (tt0) REVERT: H 107 ILE cc_start: 0.8331 (mm) cc_final: 0.8067 (mt) REVERT: H 164 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6603 (mtp180) REVERT: H 176 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.4145 (tm-30) REVERT: H 181 PHE cc_start: 0.4553 (OUTLIER) cc_final: 0.4169 (p90) REVERT: I 3 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4565 (mt) REVERT: I 75 PHE cc_start: 0.6484 (m-80) cc_final: 0.6235 (m-80) REVERT: I 110 ARG cc_start: 0.5653 (tpm170) cc_final: 0.4700 (tpm170) REVERT: I 198 CYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5279 (t) REVERT: I 217 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7300 (mttp) REVERT: I 237 HIS cc_start: 0.7771 (p90) cc_final: 0.7424 (p-80) REVERT: I 326 LEU cc_start: 0.8344 (mt) cc_final: 0.8127 (mp) REVERT: J 43 ASP cc_start: 0.7383 (m-30) cc_final: 0.7057 (m-30) REVERT: J 348 LEU cc_start: 0.4427 (OUTLIER) cc_final: 0.3828 (pp) outliers start: 147 outliers final: 105 residues processed: 413 average time/residue: 0.4239 time to fit residues: 289.9810 Evaluate side-chains 391 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 278 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 499 SER 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 557 MET Chi-restraints excluded: chain G residue 574 GLU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 277 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 29814 Z= 0.353 Angle : 0.793 14.939 40742 Z= 0.409 Chirality : 0.047 0.232 4503 Planarity : 0.005 0.061 5002 Dihedral : 14.931 178.704 4664 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.18 % Favored : 83.03 % Rotamer: Outliers : 4.86 % Allowed : 16.54 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 1.07 % 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: -3.32 (0.13), residues: 3400 helix: -0.96 (0.17), residues: 945 sheet: -0.71 (0.23), residues: 501 loop : -3.47 (0.12), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 203 HIS 0.007 0.001 HIS B 84 PHE 0.019 0.002 PHE A 89 TYR 0.021 0.002 TYR G 197 ARG 0.005 0.000 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 290 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8081 (tp40) cc_final: 0.7812 (tp-100) REVERT: A 307 PHE cc_start: 0.8042 (m-10) cc_final: 0.7656 (m-10) REVERT: B 23 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8620 (m) REVERT: B 99 GLN cc_start: 0.8272 (pm20) cc_final: 0.7942 (pm20) REVERT: B 138 ASN cc_start: 0.8215 (p0) cc_final: 0.7936 (p0) REVERT: B 170 ASP cc_start: 0.8105 (t0) cc_final: 0.7739 (p0) REVERT: C 252 ASP cc_start: 0.7836 (m-30) cc_final: 0.7441 (t0) REVERT: C 280 GLU cc_start: 0.7359 (tt0) cc_final: 0.6904 (tp30) REVERT: C 347 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: D 71 HIS cc_start: 0.7034 (m-70) cc_final: 0.6590 (t-170) REVERT: D 210 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7361 (ttm170) REVERT: D 291 ARG cc_start: 0.7551 (ttt90) cc_final: 0.6974 (ttp-170) REVERT: E 210 ARG cc_start: 0.7243 (ttm170) cc_final: 0.6976 (ttp80) REVERT: E 252 ASP cc_start: 0.8396 (t0) cc_final: 0.7987 (t0) REVERT: E 333 ASP cc_start: 0.7974 (m-30) cc_final: 0.7570 (m-30) REVERT: F 88 SER cc_start: 0.8119 (t) cc_final: 0.7796 (m) REVERT: F 188 SER cc_start: 0.8981 (m) cc_final: 0.8555 (p) REVERT: F 210 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.7209 (ttm170) REVERT: F 308 SER cc_start: 0.8474 (m) cc_final: 0.8231 (p) REVERT: G 21 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6562 (ptm160) REVERT: G 247 MET cc_start: 0.8170 (ttm) cc_final: 0.7768 (mtt) REVERT: G 515 ASP cc_start: 0.7629 (t70) cc_final: 0.7319 (t70) REVERT: G 622 TYR cc_start: 0.7897 (p90) cc_final: 0.7646 (p90) REVERT: H 16 ASN cc_start: 0.8281 (t0) cc_final: 0.7774 (t0) REVERT: H 63 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7340 (tptm) REVERT: H 88 ASN cc_start: 0.7382 (m-40) cc_final: 0.6799 (t0) REVERT: H 105 GLN cc_start: 0.8694 (tt0) cc_final: 0.8331 (tt0) REVERT: H 107 ILE cc_start: 0.8317 (mm) cc_final: 0.8028 (mt) REVERT: H 164 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6503 (mtp180) REVERT: I 3 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4758 (mt) REVERT: I 110 ARG cc_start: 0.5523 (tpm170) cc_final: 0.5143 (tpm170) REVERT: I 198 CYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5361 (m) REVERT: I 217 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7181 (mttm) REVERT: I 237 HIS cc_start: 0.7664 (p90) cc_final: 0.7336 (p-80) REVERT: J 43 ASP cc_start: 0.7446 (m-30) cc_final: 0.7147 (m-30) REVERT: J 100 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8567 (mmmm) outliers start: 148 outliers final: 105 residues processed: 411 average time/residue: 0.3725 time to fit residues: 249.7311 Evaluate side-chains 377 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 266 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 413 THR 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 557 MET Chi-restraints excluded: chain G residue 574 GLU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 0.0000 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 131 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29814 Z= 0.199 Angle : 0.731 13.787 40742 Z= 0.374 Chirality : 0.044 0.230 4503 Planarity : 0.005 0.065 5002 Dihedral : 14.713 176.993 4664 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.68 % Allowed : 15.21 % Favored : 84.12 % Rotamer: Outliers : 3.67 % Allowed : 18.18 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.98 % 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: -3.14 (0.14), residues: 3400 helix: -0.77 (0.17), residues: 951 sheet: -0.86 (0.22), residues: 535 loop : -3.33 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 24 HIS 0.007 0.001 HIS B 84 PHE 0.014 0.001 PHE A 89 TYR 0.020 0.001 TYR I 390 ARG 0.007 0.000 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 304 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8037 (tp40) cc_final: 0.7780 (tp-100) REVERT: A 346 MET cc_start: 0.7051 (tpp) cc_final: 0.5152 (tpp) REVERT: B 6 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7775 (t0) REVERT: B 23 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (m) REVERT: B 99 GLN cc_start: 0.8263 (pm20) cc_final: 0.7938 (pm20) REVERT: B 138 ASN cc_start: 0.7923 (p0) cc_final: 0.7590 (t0) REVERT: C 102 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7916 (mttp) REVERT: C 252 ASP cc_start: 0.7826 (m-30) cc_final: 0.7406 (t0) REVERT: C 280 GLU cc_start: 0.7138 (tt0) cc_final: 0.6743 (tp30) REVERT: C 347 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: D 71 HIS cc_start: 0.6957 (m-70) cc_final: 0.6572 (t-170) REVERT: D 210 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7381 (ttm170) REVERT: D 291 ARG cc_start: 0.7474 (ttt90) cc_final: 0.6939 (ttp-170) REVERT: E 210 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6972 (ttp80) REVERT: E 252 ASP cc_start: 0.8402 (t0) cc_final: 0.7977 (t0) REVERT: E 333 ASP cc_start: 0.7948 (m-30) cc_final: 0.7572 (m-30) REVERT: F 37 ARG cc_start: 0.7300 (ttp80) cc_final: 0.7066 (ttp80) REVERT: F 88 SER cc_start: 0.8031 (t) cc_final: 0.7732 (m) REVERT: F 135 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (p0) REVERT: F 188 SER cc_start: 0.8853 (m) cc_final: 0.8427 (p) REVERT: F 210 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7215 (ttm170) REVERT: G 21 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6506 (ptm160) REVERT: G 247 MET cc_start: 0.8093 (ttm) cc_final: 0.7688 (mtt) REVERT: G 515 ASP cc_start: 0.7535 (t70) cc_final: 0.7203 (t0) REVERT: G 622 TYR cc_start: 0.7800 (p90) cc_final: 0.7516 (p90) REVERT: H 16 ASN cc_start: 0.8306 (t0) cc_final: 0.8013 (t0) REVERT: H 63 LYS cc_start: 0.7722 (tmmt) cc_final: 0.7396 (tptm) REVERT: H 88 ASN cc_start: 0.7367 (m-40) cc_final: 0.6800 (t0) REVERT: H 105 GLN cc_start: 0.8572 (tt0) cc_final: 0.8232 (tt0) REVERT: H 107 ILE cc_start: 0.8293 (mm) cc_final: 0.8036 (mt) REVERT: H 164 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6400 (mtp180) REVERT: H 176 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.4734 (pt0) REVERT: I 3 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4743 (mt) REVERT: I 99 MET cc_start: 0.6489 (mtp) cc_final: 0.6196 (mtt) REVERT: I 110 ARG cc_start: 0.5038 (tpm170) cc_final: 0.4185 (tpm170) REVERT: I 198 CYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5442 (t) REVERT: I 204 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7301 (tt) REVERT: I 217 LYS cc_start: 0.7514 (mtpt) cc_final: 0.7183 (mttm) REVERT: I 237 HIS cc_start: 0.7665 (p90) cc_final: 0.7395 (p-80) REVERT: J 43 ASP cc_start: 0.7342 (m-30) cc_final: 0.7050 (m-30) REVERT: J 100 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8542 (mmmm) outliers start: 112 outliers final: 85 residues processed: 393 average time/residue: 0.3823 time to fit residues: 243.9622 Evaluate side-chains 371 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 276 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 100 optimal weight: 0.0980 chunk 65 optimal weight: 0.0770 chunk 64 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 overall best weight: 1.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 160 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29814 Z= 0.208 Angle : 0.732 13.722 40742 Z= 0.373 Chirality : 0.044 0.237 4503 Planarity : 0.005 0.066 5002 Dihedral : 14.598 177.504 4662 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.68 % Allowed : 15.06 % Favored : 84.26 % Rotamer: Outliers : 3.74 % Allowed : 18.44 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % 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: -3.04 (0.14), residues: 3400 helix: -0.70 (0.17), residues: 950 sheet: -0.77 (0.22), residues: 548 loop : -3.29 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 24 HIS 0.017 0.001 HIS F 315 PHE 0.014 0.001 PHE A 89 TYR 0.021 0.001 TYR A 175 ARG 0.005 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 290 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6849 (pp30) REVERT: A 346 MET cc_start: 0.7037 (tpp) cc_final: 0.5155 (tpp) REVERT: B 6 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7789 (t0) REVERT: B 23 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 99 GLN cc_start: 0.8292 (pm20) cc_final: 0.7977 (pm20) REVERT: B 138 ASN cc_start: 0.7884 (p0) cc_final: 0.7654 (t0) REVERT: C 252 ASP cc_start: 0.7819 (m-30) cc_final: 0.7408 (t0) REVERT: C 280 GLU cc_start: 0.6995 (tt0) cc_final: 0.6684 (tp30) REVERT: C 347 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: D 71 HIS cc_start: 0.6981 (m-70) cc_final: 0.6579 (t-170) REVERT: D 210 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7350 (ttm170) REVERT: D 280 GLU cc_start: 0.7422 (tt0) cc_final: 0.6863 (pm20) REVERT: D 291 ARG cc_start: 0.7509 (ttt90) cc_final: 0.6972 (ttp-170) REVERT: E 44 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7371 (mm-30) REVERT: E 210 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6948 (ttp80) REVERT: E 252 ASP cc_start: 0.8417 (t0) cc_final: 0.7998 (t0) REVERT: E 333 ASP cc_start: 0.7994 (m-30) cc_final: 0.7629 (m-30) REVERT: F 37 ARG cc_start: 0.7272 (ttp80) cc_final: 0.7039 (ttp80) REVERT: F 88 SER cc_start: 0.8073 (t) cc_final: 0.7779 (m) REVERT: F 135 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7433 (p0) REVERT: F 188 SER cc_start: 0.8871 (m) cc_final: 0.8440 (p) REVERT: F 210 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7186 (ttm170) REVERT: G 21 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6525 (ptm160) REVERT: G 247 MET cc_start: 0.8091 (ttm) cc_final: 0.7716 (mtt) REVERT: G 515 ASP cc_start: 0.7598 (t70) cc_final: 0.7291 (t0) REVERT: G 584 ARG cc_start: 0.7483 (tpp80) cc_final: 0.7221 (tpp80) REVERT: G 622 TYR cc_start: 0.7738 (p90) cc_final: 0.7420 (p90) REVERT: H 16 ASN cc_start: 0.8323 (t0) cc_final: 0.8030 (t0) REVERT: H 63 LYS cc_start: 0.7764 (tmmt) cc_final: 0.7447 (tptm) REVERT: H 88 ASN cc_start: 0.7392 (m-40) cc_final: 0.6794 (t0) REVERT: H 105 GLN cc_start: 0.8626 (tt0) cc_final: 0.8257 (tt0) REVERT: H 107 ILE cc_start: 0.8278 (mm) cc_final: 0.8022 (mt) REVERT: H 164 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6433 (mtp180) REVERT: H 176 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.4839 (pt0) REVERT: I 3 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4762 (mt) REVERT: I 99 MET cc_start: 0.6463 (mtp) cc_final: 0.6152 (mtt) REVERT: I 110 ARG cc_start: 0.4893 (tpm170) cc_final: 0.4029 (tpm170) REVERT: I 198 CYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5983 (p) REVERT: J 43 ASP cc_start: 0.7460 (m-30) cc_final: 0.7145 (m-30) outliers start: 114 outliers final: 90 residues processed: 381 average time/residue: 0.3793 time to fit residues: 235.3770 Evaluate side-chains 375 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 275 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.8980 chunk 318 optimal weight: 30.0000 chunk 290 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 308 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 114 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29814 Z= 0.221 Angle : 0.730 13.582 40742 Z= 0.373 Chirality : 0.045 0.348 4503 Planarity : 0.005 0.067 5002 Dihedral : 14.532 177.633 4662 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 15.59 % Favored : 83.82 % Rotamer: Outliers : 3.77 % Allowed : 18.50 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % 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: -2.97 (0.14), residues: 3400 helix: -0.66 (0.17), residues: 949 sheet: -0.70 (0.22), residues: 548 loop : -3.24 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 24 HIS 0.007 0.001 HIS B 84 PHE 0.022 0.001 PHE H 84 TYR 0.030 0.001 TYR G 197 ARG 0.005 0.000 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 281 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.6936 (tpp) cc_final: 0.5103 (tpp) REVERT: B 6 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7808 (t0) REVERT: B 23 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8572 (m) REVERT: B 99 GLN cc_start: 0.8343 (pm20) cc_final: 0.8052 (pm20) REVERT: C 252 ASP cc_start: 0.7808 (m-30) cc_final: 0.7453 (t0) REVERT: C 280 GLU cc_start: 0.7011 (tt0) cc_final: 0.6654 (tp30) REVERT: C 347 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: D 43 MET cc_start: 0.7185 (mmt) cc_final: 0.6828 (mmt) REVERT: D 71 HIS cc_start: 0.6990 (m-70) cc_final: 0.6587 (t-170) REVERT: D 210 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7445 (ttm170) REVERT: D 280 GLU cc_start: 0.7315 (tt0) cc_final: 0.6873 (pm20) REVERT: D 291 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7000 (ttp-170) REVERT: E 44 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7251 (mm-30) REVERT: E 252 ASP cc_start: 0.8381 (t0) cc_final: 0.7961 (t0) REVERT: E 333 ASP cc_start: 0.7980 (m-30) cc_final: 0.7624 (m-30) REVERT: F 37 ARG cc_start: 0.7290 (ttp80) cc_final: 0.7062 (ttp80) REVERT: F 88 SER cc_start: 0.8035 (t) cc_final: 0.7738 (m) REVERT: F 135 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7394 (p0) REVERT: F 188 SER cc_start: 0.8862 (m) cc_final: 0.8433 (p) REVERT: F 210 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7182 (ttm170) REVERT: G 21 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6625 (ptm160) REVERT: G 247 MET cc_start: 0.8100 (ttm) cc_final: 0.7766 (mtt) REVERT: G 515 ASP cc_start: 0.7583 (t70) cc_final: 0.7265 (t0) REVERT: G 622 TYR cc_start: 0.7594 (p90) cc_final: 0.7275 (p90) REVERT: H 63 LYS cc_start: 0.7775 (tmmt) cc_final: 0.7450 (tptm) REVERT: H 88 ASN cc_start: 0.7388 (m-40) cc_final: 0.6783 (t0) REVERT: H 105 GLN cc_start: 0.8655 (tt0) cc_final: 0.8363 (tt0) REVERT: H 107 ILE cc_start: 0.8277 (mm) cc_final: 0.8018 (mt) REVERT: H 164 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6468 (mtp180) REVERT: H 176 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4758 (pt0) REVERT: I 3 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.4663 (mt) REVERT: I 99 MET cc_start: 0.6530 (mtp) cc_final: 0.6214 (mtt) REVERT: I 110 ARG cc_start: 0.5093 (tpm170) cc_final: 0.4189 (tpm170) REVERT: I 198 CYS cc_start: 0.6246 (OUTLIER) cc_final: 0.6002 (p) REVERT: I 258 GLU cc_start: 0.8139 (tp30) cc_final: 0.7892 (tm-30) REVERT: J 43 ASP cc_start: 0.7361 (m-30) cc_final: 0.7093 (m-30) outliers start: 115 outliers final: 93 residues processed: 374 average time/residue: 0.3938 time to fit residues: 239.7437 Evaluate side-chains 368 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 266 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 211 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 110 GLN B 72 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 29814 Z= 0.534 Angle : 0.886 13.940 40742 Z= 0.457 Chirality : 0.052 0.321 4503 Planarity : 0.006 0.064 5002 Dihedral : 14.854 179.591 4662 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.97 % Favored : 82.35 % Rotamer: Outliers : 3.90 % Allowed : 18.54 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.98 % 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: -3.29 (0.14), residues: 3400 helix: -1.05 (0.17), residues: 964 sheet: -0.60 (0.22), residues: 515 loop : -3.44 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 142 HIS 0.021 0.002 HIS F 315 PHE 0.025 0.002 PHE F 89 TYR 0.026 0.002 TYR G 197 ARG 0.007 0.001 ARG F 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 258 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TRP cc_start: 0.8546 (t-100) cc_final: 0.8269 (t-100) REVERT: A 307 PHE cc_start: 0.8117 (m-10) cc_final: 0.7883 (m-10) REVERT: B 6 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7852 (t0) REVERT: B 23 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8653 (m) REVERT: B 96 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 99 GLN cc_start: 0.8426 (pm20) cc_final: 0.8141 (pm20) REVERT: C 252 ASP cc_start: 0.7842 (m-30) cc_final: 0.7508 (t0) REVERT: C 347 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: D 71 HIS cc_start: 0.7024 (m-70) cc_final: 0.6581 (t-170) REVERT: D 291 ARG cc_start: 0.7587 (ttt90) cc_final: 0.7005 (ttp-170) REVERT: E 210 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6958 (ttp80) REVERT: E 252 ASP cc_start: 0.8401 (t0) cc_final: 0.7957 (t0) REVERT: E 333 ASP cc_start: 0.8013 (m-30) cc_final: 0.7598 (m-30) REVERT: F 88 SER cc_start: 0.8128 (t) cc_final: 0.7808 (m) REVERT: F 188 SER cc_start: 0.9082 (m) cc_final: 0.8675 (p) REVERT: G 14 ASP cc_start: 0.4195 (OUTLIER) cc_final: 0.3979 (p0) REVERT: G 21 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6815 (ptm160) REVERT: G 515 ASP cc_start: 0.7684 (t70) cc_final: 0.7339 (t0) REVERT: G 622 TYR cc_start: 0.7823 (p90) cc_final: 0.7480 (p90) REVERT: H 63 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7337 (tptm) REVERT: H 88 ASN cc_start: 0.7434 (m-40) cc_final: 0.6803 (t0) REVERT: H 105 GLN cc_start: 0.8698 (tt0) cc_final: 0.8394 (tt0) REVERT: H 107 ILE cc_start: 0.8353 (mm) cc_final: 0.7985 (mt) REVERT: H 164 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6704 (mtp180) REVERT: H 176 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.4973 (pt0) REVERT: I 99 MET cc_start: 0.6682 (mtp) cc_final: 0.6382 (mtt) REVERT: I 198 CYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5501 (m) REVERT: I 311 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (tt) outliers start: 119 outliers final: 95 residues processed: 361 average time/residue: 0.3868 time to fit residues: 226.4788 Evaluate side-chains 350 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 246 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 574 GLU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 227 TRP Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 274 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 101 GLN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 338 GLN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114579 restraints weight = 44274.756| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.83 r_work: 0.3067 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29814 Z= 0.202 Angle : 0.755 15.170 40742 Z= 0.384 Chirality : 0.045 0.295 4503 Planarity : 0.005 0.065 5002 Dihedral : 14.659 177.437 4662 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.68 % Favored : 84.79 % Rotamer: Outliers : 2.92 % Allowed : 19.62 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % 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: -3.04 (0.14), residues: 3400 helix: -0.80 (0.17), residues: 957 sheet: -0.61 (0.22), residues: 532 loop : -3.28 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 24 HIS 0.012 0.001 HIS G 272 PHE 0.017 0.001 PHE H 84 TYR 0.023 0.001 TYR G 197 ARG 0.005 0.000 ARG I 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6287.95 seconds wall clock time: 114 minutes 32.94 seconds (6872.94 seconds total)