Starting phenix.real_space_refine on Wed Jun 25 08:49:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.map" model { file = "/net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lnb_0929/06_2025/6lnb_0929.cif" } resolution = 3.18 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= 0.004 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 99 5.49 5 S 146 5.16 5 C 18473 2.51 5 N 5119 2.21 5 O 5746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29583 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2725 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2685 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2681 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 2 Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2659 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2443 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 284} Chain breaks: 3 Chain: "H" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4001 Classifications: {'peptide': 510} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 485} Chain breaks: 2 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2937 Classifications: {'peptide': 359} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 339} Chain breaks: 3 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 17} Link IDs: {'rna2p': 22, 'rna3p': 37} Chain: "N" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 678 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "O" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "I" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 17.08, per 1000 atoms: 0.58 Number of scatterers: 29583 At special positions: 0 Unit cell: (194.4, 158.76, 163.08, 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 146 16.00 P 99 15.00 O 5746 8.00 N 5119 7.00 C 18473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6522 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 42 sheets defined 28.8% alpha, 12.4% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 9.66 Creating SS restraints... Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.542A pdb=" N LEU G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 105 through 123 removed outlier: 3.742A pdb=" N THR G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.621A pdb=" N ARG G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.961A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 197 " --> pdb=" O MET G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 269 removed outlier: 3.882A pdb=" N GLY G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 269 " --> pdb=" O GLY G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 313 removed outlier: 4.294A pdb=" N LEU G 310 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN G 311 " --> pdb=" O SER G 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA G 313 " --> pdb=" O LEU G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 321 removed outlier: 3.505A pdb=" N LEU G 320 " --> pdb=" O TYR G 316 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 321 " --> pdb=" O ILE G 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 316 through 321' Processing helix chain 'G' and resid 331 through 344 removed outlier: 3.658A pdb=" N LEU G 337 " --> pdb=" O ASP G 333 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 342 " --> pdb=" O MET G 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.798A pdb=" N ALA F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.675A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.807A pdb=" N ARG F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.702A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.095A pdb=" N MET F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 197 " --> pdb=" O MET F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.548A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.800A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.527A pdb=" N TYR F 316 " --> pdb=" O GLN F 312 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 312 through 318' Processing helix chain 'F' and resid 328 through 343 removed outlier: 3.722A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.946A pdb=" N GLN E 67 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 113 removed outlier: 3.794A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.613A pdb=" N GLU E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.717A pdb=" N ARG E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.537A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.609A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 removed outlier: 3.533A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.924A pdb=" N GLN E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 321 removed outlier: 3.716A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.734A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 removed outlier: 3.605A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY E 344 " --> pdb=" O ASN E 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.515A pdb=" N LEU D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.622A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.666A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 138 " --> pdb=" O MET D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.818A pdb=" N LEU D 142 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP D 143 " --> pdb=" O LYS D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 139 through 143' Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.517A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 182' Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.581A pdb=" N LYS D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 197 " --> pdb=" O MET D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 266 removed outlier: 3.603A pdb=" N THR D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.652A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.535A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.814A pdb=" N GLN C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.912A pdb=" N THR C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 4.072A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 183' Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.825A pdb=" N LYS C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.780A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.517A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.649A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.619A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 342 " --> pdb=" O MET C 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.678A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.894A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.671A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.638A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.794A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.301A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'H' and resid 15 through 18 removed outlier: 4.030A pdb=" N GLU H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 15 through 18' Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.719A pdb=" N ARG H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 44 removed outlier: 4.250A pdb=" N ILE H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.961A pdb=" N SER H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 3.664A pdb=" N VAL H 130 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN H 131 " --> pdb=" O LYS H 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 131' Processing helix chain 'H' and resid 174 through 181 removed outlier: 3.781A pdb=" N ALA H 178 " --> pdb=" O CYS H 174 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 227 Processing helix chain 'H' and resid 249 through 254 removed outlier: 3.830A pdb=" N CYS H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 427 removed outlier: 3.751A pdb=" N PHE H 415 " --> pdb=" O SER H 411 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 419 " --> pdb=" O PHE H 415 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE H 422 " --> pdb=" O PHE H 418 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE H 426 " --> pdb=" O PHE H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 499 Processing helix chain 'H' and resid 527 through 531 removed outlier: 3.563A pdb=" N SER H 531 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 561 removed outlier: 4.102A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU H 559 " --> pdb=" O ALA H 555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 586 removed outlier: 4.260A pdb=" N TYR H 586 " --> pdb=" O LEU H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 612 removed outlier: 3.608A pdb=" N THR H 611 " --> pdb=" O ASP H 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.634A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 28 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.801A pdb=" N ARG A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 removed outlier: 3.929A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 Processing helix chain 'J' and resid 48 through 52 removed outlier: 4.218A pdb=" N THR J 51 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE J 52 " --> pdb=" O TYR J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 52' Processing helix chain 'J' and resid 67 through 77 removed outlier: 3.898A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.615A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.812A pdb=" N HIS J 225 " --> pdb=" O TRP J 221 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 removed outlier: 3.644A pdb=" N GLN J 242 " --> pdb=" O PHE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 255 removed outlier: 4.382A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 328 through 333 Processing helix chain 'J' and resid 338 through 343 removed outlier: 3.541A pdb=" N VAL J 343 " --> pdb=" O ILE J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 380 removed outlier: 3.517A pdb=" N CYS J 374 " --> pdb=" O GLY J 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.563A pdb=" N PHE I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 45 Processing helix chain 'I' and resid 46 through 50 removed outlier: 4.183A pdb=" N GLN I 50 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.621A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.511A pdb=" N LEU I 132 " --> pdb=" O CYS I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.868A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS I 143 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 139 through 144' Processing helix chain 'I' and resid 196 through 202 Processing helix chain 'I' and resid 219 through 232 removed outlier: 3.555A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 246 Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.923A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU I 263 " --> pdb=" O VAL I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 302 removed outlier: 3.553A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 310 removed outlier: 3.522A pdb=" N ARG I 310 " --> pdb=" O TYR I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 332 removed outlier: 3.995A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.553A pdb=" N ALA I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.645A pdb=" N CYS I 374 " --> pdb=" O GLY I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 391 removed outlier: 3.775A pdb=" N TYR I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 391 " --> pdb=" O SER I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 391' Processing sheet with id=AA1, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.863A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 211 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS G 151 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.539A pdb=" N ASN G 35 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'G' and resid 270 through 272 removed outlier: 3.521A pdb=" N ASP G 272 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.995A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AB1, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.691A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.515A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AB7, first strand: chain 'D' and resid 8 through 9 removed outlier: 3.865A pdb=" N GLY D 345 " --> pdb=" O TYR D 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.747A pdb=" N ARG D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC2, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.796A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 41 removed outlier: 3.757A pdb=" N HIS C 71 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AC6, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AC7, first strand: chain 'B' and resid 8 through 9 removed outlier: 3.574A pdb=" N GLY B 345 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.560A pdb=" N CYS B 19 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 88 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 166 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.598A pdb=" N THR A 144 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 248 through 251 removed outlier: 3.520A pdb=" N GLU B 254 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AD3, first strand: chain 'H' and resid 85 through 86 removed outlier: 4.017A pdb=" N ALA H 217 " --> pdb=" O ASN H 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AD5, first strand: chain 'H' and resid 201 through 204 removed outlier: 8.603A pdb=" N ALA H 589 " --> pdb=" O TYR H 210 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER H 212 " --> pdb=" O ALA H 589 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA H 591 " --> pdb=" O SER H 212 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER H 214 " --> pdb=" O ALA H 591 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS H 593 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE H 590 " --> pdb=" O LEU H 572 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU H 572 " --> pdb=" O ILE H 590 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU H 592 " --> pdb=" O TYR H 570 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR H 570 " --> pdb=" O GLU H 592 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE H 594 " --> pdb=" O VAL H 568 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 566 " --> pdb=" O GLY H 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 439 through 444 removed outlier: 6.494A pdb=" N VAL H 478 " --> pdb=" O HIS H 443 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU H 481 " --> pdb=" O PRO H 391 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU H 483 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL H 389 " --> pdb=" O LEU H 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 398 through 399 Processing sheet with id=AD8, first strand: chain 'H' and resid 457 through 458 removed outlier: 3.635A pdb=" N SER H 465 " --> pdb=" O VAL H 457 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 614 through 616 removed outlier: 3.720A pdb=" N GLN H 626 " --> pdb=" O SER H 615 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.575A pdb=" N TYR A 5 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 90 " --> pdb=" O TYR A 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 101 through 103 removed outlier: 4.360A pdb=" N ARG A 102 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 168 " --> pdb=" O ARG A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'A' and resid 152 through 155 Processing sheet with id=AE4, first strand: chain 'J' and resid 108 through 109 removed outlier: 4.325A pdb=" N VAL J 108 " --> pdb=" O PHE J 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AE6, first strand: chain 'I' and resid 273 through 274 removed outlier: 6.629A pdb=" N LEU I 273 " --> pdb=" O LYS I 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 672 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 9.97 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7733 1.33 - 1.45: 7137 1.45 - 1.58: 15267 1.58 - 1.70: 197 1.70 - 1.82: 209 Bond restraints: 30543 Sorted by residual: bond pdb=" C1' U M 39 " pdb=" N1 U M 39 " ideal model delta sigma weight residual 1.480 1.560 -0.080 1.50e-02 4.44e+03 2.85e+01 bond pdb=" C LYS I 210 " pdb=" N PRO I 211 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" N VAL J 30 " pdb=" CA VAL J 30 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N ASP J 29 " pdb=" CA ASP J 29 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 bond pdb=" N TYR J 27 " pdb=" CA TYR J 27 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 7.02e+00 ... (remaining 30538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 40964 2.96 - 5.92: 780 5.92 - 8.88: 121 8.88 - 11.83: 19 11.83 - 14.79: 14 Bond angle restraints: 41898 Sorted by residual: angle pdb=" C GLU H 575 " pdb=" N PRO H 576 " pdb=" CA PRO H 576 " ideal model delta sigma weight residual 127.00 141.42 -14.42 2.40e+00 1.74e-01 3.61e+01 angle pdb=" C CYS G 103 " pdb=" N ASN G 104 " pdb=" CA ASN G 104 " ideal model delta sigma weight residual 123.93 132.82 -8.89 1.54e+00 4.22e-01 3.33e+01 angle pdb=" C GLU H 575 " pdb=" N PRO H 576 " pdb=" CD PRO H 576 " ideal model delta sigma weight residual 120.60 107.91 12.69 2.20e+00 2.07e-01 3.33e+01 angle pdb=" C LEU C 142 " pdb=" N TRP C 143 " pdb=" CA TRP C 143 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" N ARG J 39 " pdb=" CA ARG J 39 " pdb=" C ARG J 39 " ideal model delta sigma weight residual 111.69 105.14 6.55 1.23e+00 6.61e-01 2.83e+01 ... (remaining 41893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 17705 35.63 - 71.26: 389 71.26 - 106.89: 30 106.89 - 142.53: 1 142.53 - 178.16: 3 Dihedral angle restraints: 18128 sinusoidal: 8090 harmonic: 10038 Sorted by residual: dihedral pdb=" CA LYS J 7 " pdb=" C LYS J 7 " pdb=" N PRO J 8 " pdb=" CA PRO J 8 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 50.16 -178.16 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual 232.00 78.43 153.57 1 1.70e+01 3.46e-03 6.30e+01 ... (remaining 18125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4136 0.092 - 0.184: 466 0.184 - 0.276: 26 0.276 - 0.368: 1 0.368 - 0.460: 2 Chirality restraints: 4631 Sorted by residual: chirality pdb=" CB ILE J 94 " pdb=" CA ILE J 94 " pdb=" CG1 ILE J 94 " pdb=" CG2 ILE J 94 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CB ILE H 534 " pdb=" CA ILE H 534 " pdb=" CG1 ILE H 534 " pdb=" CG2 ILE H 534 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASP J 29 " pdb=" N ASP J 29 " pdb=" C ASP J 29 " pdb=" CB ASP J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4628 not shown) Planarity restraints: 5001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 9 " 0.019 2.00e-02 2.50e+03 2.18e-02 9.49e+00 pdb=" CG TYR D 9 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 9 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR D 9 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 9 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 9 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR D 9 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 9 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 289 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO J 290 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 290 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 290 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " -0.016 2.00e-02 2.50e+03 1.84e-02 6.81e+00 pdb=" CG TYR F 9 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " -0.000 2.00e-02 2.50e+03 ... (remaining 4998 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2739 2.74 - 3.28: 26326 3.28 - 3.82: 46427 3.82 - 4.36: 56459 4.36 - 4.90: 95932 Nonbonded interactions: 227883 Sorted by model distance: nonbonded pdb=" OG SER A 187 " pdb=" O GLN A 194 " model vdw 2.202 3.040 nonbonded pdb=" CD2 LEU J 3 " pdb=" CZ PHE J 33 " model vdw 2.223 3.760 nonbonded pdb=" O TYR G 9 " pdb=" O2' U M 5 " model vdw 2.246 3.040 nonbonded pdb=" O SER H 133 " pdb=" OG1 THR H 137 " model vdw 2.262 3.040 nonbonded pdb=" OG SER J 102 " pdb=" O ILE J 287 " model vdw 2.262 3.040 ... (remaining 227878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 228 or resid 243 through 349)) selection = (chain 'C' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'D' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'E' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'F' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'G' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) } ncs_group { reference = (chain 'I' and (resid 1 through 172 or resid 195 through 232 or resid 236 throug \ h 393)) selection = chain 'J' } 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: 1.160 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: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 69.300 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.006 0.080 30543 Z= 0.282 Angle : 1.070 14.792 41898 Z= 0.576 Chirality : 0.059 0.460 4631 Planarity : 0.008 0.069 5001 Dihedral : 14.600 178.157 11606 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.50 % Allowed : 3.64 % Favored : 95.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % Twisted General : 0.15 % 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: -5.23 (0.11), residues: 3369 helix: -4.69 (0.06), residues: 887 sheet: -1.77 (0.21), residues: 533 loop : -3.50 (0.11), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 159 HIS 0.024 0.002 HIS C 290 PHE 0.033 0.003 PHE A 10 TYR 0.050 0.004 TYR D 9 ARG 0.017 0.001 ARG G 286 Details of bonding type rmsd hydrogen bonds : bond 0.30620 ( 714) hydrogen bonds : angle 10.39606 ( 1920) covalent geometry : bond 0.00611 (30543) covalent geometry : angle 1.06968 (41898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 461 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 229 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6460 (tt0) REVERT: G 301 SER cc_start: 0.8497 (p) cc_final: 0.8230 (m) REVERT: G 309 ILE cc_start: 0.8431 (mt) cc_final: 0.8160 (mm) REVERT: G 338 MET cc_start: 0.8325 (mmt) cc_final: 0.8012 (mmt) REVERT: G 349 HIS cc_start: 0.6045 (t70) cc_final: 0.5822 (t-170) REVERT: F 180 ASP cc_start: 0.7372 (m-30) cc_final: 0.7018 (m-30) REVERT: E 35 ASN cc_start: 0.8055 (m-40) cc_final: 0.7617 (m110) REVERT: E 63 GLU cc_start: 0.7555 (tp30) cc_final: 0.7119 (tt0) REVERT: E 202 ASP cc_start: 0.7124 (p0) cc_final: 0.6728 (t0) REVERT: D 110 GLN cc_start: 0.6972 (mp-120) cc_final: 0.6723 (mm-40) REVERT: D 217 THR cc_start: 0.8610 (p) cc_final: 0.8399 (t) REVERT: D 228 THR cc_start: 0.6964 (t) cc_final: 0.6759 (p) REVERT: C 74 ASP cc_start: 0.8123 (m-30) cc_final: 0.7870 (m-30) REVERT: C 165 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7372 (mtmm) REVERT: C 210 ARG cc_start: 0.6961 (tpp80) cc_final: 0.6716 (ttm-80) REVERT: B 148 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7072 (tppt) REVERT: H 63 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4747 (mttt) REVERT: H 93 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6038 (ptt90) REVERT: H 526 GLU cc_start: 0.6849 (mp0) cc_final: 0.6417 (mp0) REVERT: H 535 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7026 (mm-30) REVERT: H 558 THR cc_start: 0.5874 (t) cc_final: 0.5559 (m) outliers start: 15 outliers final: 4 residues processed: 475 average time/residue: 0.4935 time to fit residues: 355.9908 Evaluate side-chains 276 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 278 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 30.0000 chunk 263 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 184 ASN F 135 ASN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN E 183 ASN E 184 ASN E 290 HIS D 104 ASN D 110 GLN D 145 ASN D 299 HIS C 145 ASN C 162 ASN C 290 HIS C 340 ASN B 104 ASN B 174 ASN B 348 GLN B 349 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 HIS H 548 ASN H 581 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS A 85 HIS A 143 HIS A 150 HIS A 178 ASN J 153 HIS J 237 HIS J 351 ASN I 23 ASN I 25 ASN I 31 HIS I 154 ASN I 207 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.208381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153327 restraints weight = 38217.053| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.51 r_work: 0.3221 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30543 Z= 0.207 Angle : 0.752 9.865 41898 Z= 0.400 Chirality : 0.047 0.220 4631 Planarity : 0.007 0.076 5001 Dihedral : 16.778 174.368 5088 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 2.08 % Allowed : 7.54 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % Twisted General : 0.00 % 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: -4.32 (0.12), residues: 3369 helix: -3.35 (0.12), residues: 926 sheet: -1.04 (0.23), residues: 495 loop : -3.26 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 159 HIS 0.014 0.002 HIS C 290 PHE 0.025 0.002 PHE A 10 TYR 0.027 0.002 TYR D 9 ARG 0.008 0.001 ARG C 298 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 714) hydrogen bonds : angle 6.04345 ( 1920) covalent geometry : bond 0.00480 (30543) covalent geometry : angle 0.75201 (41898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 114 GLN cc_start: 0.8185 (tt0) cc_final: 0.7974 (tt0) REVERT: G 202 ASP cc_start: 0.7191 (m-30) cc_final: 0.6924 (m-30) REVERT: G 229 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7226 (tm-30) REVERT: G 349 HIS cc_start: 0.6691 (t70) cc_final: 0.6177 (t-170) REVERT: F 180 ASP cc_start: 0.7933 (m-30) cc_final: 0.7412 (m-30) REVERT: F 192 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7547 (mm-30) REVERT: F 312 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8481 (mm-40) REVERT: E 63 GLU cc_start: 0.8274 (tp30) cc_final: 0.7659 (tt0) REVERT: C 165 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7505 (mtmm) REVERT: B 176 THR cc_start: 0.7086 (p) cc_final: 0.6649 (t) REVERT: B 332 ASN cc_start: 0.8676 (m-40) cc_final: 0.8463 (t0) REVERT: H 63 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.4603 (mttt) REVERT: H 93 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.5880 (ptt90) REVERT: H 535 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6621 (mm-30) REVERT: H 587 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6780 (mmtm) REVERT: A 142 GLU cc_start: 0.5302 (mm-30) cc_final: 0.4957 (mm-30) REVERT: I 323 MET cc_start: 0.4752 (mpp) cc_final: 0.4481 (mpp) outliers start: 63 outliers final: 36 residues processed: 333 average time/residue: 0.4206 time to fit residues: 222.1252 Evaluate side-chains 285 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 587 LYS Chi-restraints excluded: chain H residue 614 TRP Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 198 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 331 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS F 114 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN C 349 HIS B 335 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.210591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154789 restraints weight = 38192.130| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.71 r_work: 0.3259 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30543 Z= 0.156 Angle : 0.656 8.410 41898 Z= 0.349 Chirality : 0.044 0.211 4631 Planarity : 0.006 0.064 5001 Dihedral : 16.576 175.927 5088 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 2.45 % Allowed : 9.26 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -3.64 (0.13), residues: 3369 helix: -2.45 (0.15), residues: 930 sheet: -0.83 (0.23), residues: 517 loop : -2.97 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 143 HIS 0.008 0.001 HIS B 84 PHE 0.025 0.002 PHE A 10 TYR 0.021 0.002 TYR J 62 ARG 0.005 0.001 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 714) hydrogen bonds : angle 5.35463 ( 1920) covalent geometry : bond 0.00357 (30543) covalent geometry : angle 0.65607 (41898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 3.026 Fit side-chains REVERT: G 202 ASP cc_start: 0.7028 (m-30) cc_final: 0.6800 (m-30) REVERT: G 229 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7098 (tt0) REVERT: G 349 HIS cc_start: 0.6702 (t70) cc_final: 0.6267 (t-170) REVERT: F 180 ASP cc_start: 0.7859 (m-30) cc_final: 0.7424 (m-30) REVERT: F 312 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8498 (mm-40) REVERT: E 63 GLU cc_start: 0.7996 (tp30) cc_final: 0.7507 (tt0) REVERT: E 96 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: E 104 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8320 (t0) REVERT: C 165 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7230 (mtmm) REVERT: B 176 THR cc_start: 0.7077 (p) cc_final: 0.6618 (t) REVERT: B 318 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: B 332 ASN cc_start: 0.8562 (m-40) cc_final: 0.8327 (t0) REVERT: H 63 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4600 (mttt) REVERT: H 93 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.5618 (ptt90) REVERT: H 175 LYS cc_start: 0.5957 (mptt) cc_final: 0.5592 (mmmt) REVERT: H 247 MET cc_start: 0.7034 (mmm) cc_final: 0.6738 (mtm) REVERT: H 526 GLU cc_start: 0.6696 (mp0) cc_final: 0.6256 (tp30) REVERT: H 535 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6533 (mm-30) REVERT: H 587 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7083 (mmtm) REVERT: A 78 MET cc_start: 0.5226 (mtm) cc_final: 0.4713 (mtp) REVERT: A 125 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.4284 (ppp80) REVERT: A 142 GLU cc_start: 0.5030 (mm-30) cc_final: 0.4775 (mm-30) outliers start: 74 outliers final: 46 residues processed: 317 average time/residue: 0.4668 time to fit residues: 238.8724 Evaluate side-chains 289 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 587 LYS Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 614 TRP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 191 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 0.1980 chunk 335 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 272 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 327 optimal weight: 50.0000 chunk 290 optimal weight: 10.0000 chunk 343 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN B 214 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.208910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153133 restraints weight = 38235.868| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.67 r_work: 0.3203 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30543 Z= 0.189 Angle : 0.686 9.136 41898 Z= 0.363 Chirality : 0.045 0.210 4631 Planarity : 0.006 0.070 5001 Dihedral : 16.596 175.457 5087 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 3.04 % Allowed : 10.38 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -3.42 (0.13), residues: 3369 helix: -2.11 (0.15), residues: 952 sheet: -0.72 (0.23), residues: 512 loop : -2.92 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 143 HIS 0.007 0.001 HIS B 84 PHE 0.021 0.002 PHE A 10 TYR 0.019 0.002 TYR J 62 ARG 0.007 0.001 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 714) hydrogen bonds : angle 5.26477 ( 1920) covalent geometry : bond 0.00445 (30543) covalent geometry : angle 0.68579 (41898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 244 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 202 ASP cc_start: 0.7139 (m-30) cc_final: 0.6914 (m-30) REVERT: G 349 HIS cc_start: 0.6710 (t70) cc_final: 0.6253 (t-170) REVERT: F 180 ASP cc_start: 0.7867 (m-30) cc_final: 0.7401 (m-30) REVERT: F 312 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8504 (mm-40) REVERT: E 63 GLU cc_start: 0.7936 (tp30) cc_final: 0.7528 (tt0) REVERT: E 65 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8168 (mp) REVERT: E 96 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: E 104 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8398 (t0) REVERT: C 165 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7235 (mtmm) REVERT: B 176 THR cc_start: 0.7026 (p) cc_final: 0.6598 (t) REVERT: B 318 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: B 332 ASN cc_start: 0.8553 (m-40) cc_final: 0.8282 (t0) REVERT: H 63 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.4547 (mttt) REVERT: H 247 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6845 (mtm) REVERT: H 526 GLU cc_start: 0.6677 (mp0) cc_final: 0.6233 (tp30) REVERT: H 535 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6586 (mm-30) REVERT: H 587 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6769 (mmtm) REVERT: A 78 MET cc_start: 0.5126 (mtm) cc_final: 0.4630 (mtp) REVERT: A 125 ARG cc_start: 0.5170 (OUTLIER) cc_final: 0.4174 (ppp80) outliers start: 92 outliers final: 55 residues processed: 317 average time/residue: 0.4089 time to fit residues: 210.0257 Evaluate side-chains 301 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 587 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 296 optimal weight: 50.0000 chunk 85 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 316 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 195 optimal weight: 0.0270 chunk 311 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN F 186 ASN E 35 ASN H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.208733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152477 restraints weight = 37920.423| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.64 r_work: 0.3193 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30543 Z= 0.186 Angle : 0.678 8.846 41898 Z= 0.358 Chirality : 0.045 0.207 4631 Planarity : 0.006 0.063 5001 Dihedral : 16.572 175.441 5087 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.40 % Allowed : 11.11 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % Twisted General : 0.00 % 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: -3.25 (0.13), residues: 3369 helix: -1.89 (0.16), residues: 956 sheet: -0.67 (0.23), residues: 514 loop : -2.84 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.007 0.001 HIS D 335 PHE 0.021 0.002 PHE A 10 TYR 0.019 0.002 TYR J 62 ARG 0.007 0.001 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 714) hydrogen bonds : angle 5.13677 ( 1920) covalent geometry : bond 0.00438 (30543) covalent geometry : angle 0.67775 (41898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 246 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 202 ASP cc_start: 0.7305 (m-30) cc_final: 0.7031 (m-30) REVERT: G 229 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7110 (tt0) REVERT: G 334 MET cc_start: 0.7588 (mtp) cc_final: 0.7190 (mtp) REVERT: G 349 HIS cc_start: 0.6839 (t70) cc_final: 0.6350 (t-170) REVERT: F 86 GLU cc_start: 0.8060 (tp30) cc_final: 0.7814 (mm-30) REVERT: F 180 ASP cc_start: 0.8000 (m-30) cc_final: 0.7521 (m-30) REVERT: F 186 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: E 63 GLU cc_start: 0.8076 (tp30) cc_final: 0.7679 (tt0) REVERT: E 65 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8215 (mp) REVERT: E 96 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: E 104 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 165 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7461 (mtmm) REVERT: B 176 THR cc_start: 0.7085 (p) cc_final: 0.6671 (t) REVERT: B 318 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: B 332 ASN cc_start: 0.8706 (m-40) cc_final: 0.8402 (t0) REVERT: H 63 LYS cc_start: 0.5655 (OUTLIER) cc_final: 0.4666 (mttt) REVERT: H 247 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7097 (mtm) REVERT: H 526 GLU cc_start: 0.6728 (mp0) cc_final: 0.6190 (tp30) REVERT: H 535 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6610 (mm-30) REVERT: H 587 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6812 (mmtm) REVERT: H 614 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.7753 (m100) REVERT: A 78 MET cc_start: 0.5105 (mtm) cc_final: 0.4568 (mtt) REVERT: A 125 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.4214 (ppp80) REVERT: A 186 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3964 (tp) outliers start: 103 outliers final: 64 residues processed: 327 average time/residue: 0.4113 time to fit residues: 215.8505 Evaluate side-chains 310 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 235 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 587 LYS Chi-restraints excluded: chain H residue 614 TRP Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 295 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN D 183 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN H 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.208334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152216 restraints weight = 38238.817| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.68 r_work: 0.3188 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30543 Z= 0.198 Angle : 0.688 9.214 41898 Z= 0.364 Chirality : 0.046 0.207 4631 Planarity : 0.006 0.068 5001 Dihedral : 16.579 175.385 5087 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.80 % Allowed : 11.60 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -3.16 (0.13), residues: 3369 helix: -1.77 (0.16), residues: 951 sheet: -0.68 (0.23), residues: 515 loop : -2.79 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.007 0.001 HIS D 335 PHE 0.019 0.002 PHE E 347 TYR 0.017 0.002 TYR E 275 ARG 0.007 0.001 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 714) hydrogen bonds : angle 5.12666 ( 1920) covalent geometry : bond 0.00468 (30543) covalent geometry : angle 0.68783 (41898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 240 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 192 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6922 (tm-30) REVERT: G 202 ASP cc_start: 0.7156 (m-30) cc_final: 0.6941 (m-30) REVERT: G 229 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7006 (tt0) REVERT: G 349 HIS cc_start: 0.6797 (t70) cc_final: 0.6341 (t-170) REVERT: F 86 GLU cc_start: 0.7811 (tp30) cc_final: 0.7589 (mm-30) REVERT: F 180 ASP cc_start: 0.7874 (m-30) cc_final: 0.7376 (m-30) REVERT: E 63 GLU cc_start: 0.7896 (tp30) cc_final: 0.7495 (tt0) REVERT: E 65 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8160 (mp) REVERT: E 96 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: E 104 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8506 (t0) REVERT: B 176 THR cc_start: 0.7081 (p) cc_final: 0.6708 (t) REVERT: B 286 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7706 (mmt-90) REVERT: B 318 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: H 63 LYS cc_start: 0.5720 (OUTLIER) cc_final: 0.4785 (mttt) REVERT: H 247 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: H 526 GLU cc_start: 0.6613 (mp0) cc_final: 0.6073 (tp30) REVERT: A 78 MET cc_start: 0.5035 (mtm) cc_final: 0.4510 (mtt) REVERT: A 125 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.4227 (ppp80) REVERT: J 89 LEU cc_start: 0.2080 (OUTLIER) cc_final: 0.1872 (tm) outliers start: 115 outliers final: 74 residues processed: 334 average time/residue: 0.4363 time to fit residues: 235.5029 Evaluate side-chains 320 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 237 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 224 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 179 optimal weight: 0.4980 chunk 294 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 272 optimal weight: 0.0050 chunk 246 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS C 71 HIS ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 GLN I 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.212623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156617 restraints weight = 38057.209| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.80 r_work: 0.3251 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30543 Z= 0.113 Angle : 0.588 8.345 41898 Z= 0.311 Chirality : 0.042 0.215 4631 Planarity : 0.005 0.061 5001 Dihedral : 16.373 176.107 5087 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 2.41 % Allowed : 13.39 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -2.86 (0.14), residues: 3369 helix: -1.46 (0.16), residues: 956 sheet: -0.44 (0.23), residues: 504 loop : -2.65 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 143 HIS 0.005 0.001 HIS H 158 PHE 0.015 0.001 PHE A 10 TYR 0.018 0.001 TYR C 275 ARG 0.007 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 714) hydrogen bonds : angle 4.80982 ( 1920) covalent geometry : bond 0.00250 (30543) covalent geometry : angle 0.58803 (41898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 99 GLN cc_start: 0.7679 (pm20) cc_final: 0.7369 (mm-40) REVERT: G 112 LEU cc_start: 0.8007 (mm) cc_final: 0.7482 (mm) REVERT: G 123 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6460 (tt) REVERT: G 192 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7193 (tp30) REVERT: G 202 ASP cc_start: 0.7091 (m-30) cc_final: 0.6827 (m-30) REVERT: G 229 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6914 (tt0) REVERT: G 334 MET cc_start: 0.7226 (mtp) cc_final: 0.6766 (mtp) REVERT: G 349 HIS cc_start: 0.6651 (t70) cc_final: 0.6268 (t-170) REVERT: F 180 ASP cc_start: 0.7816 (m-30) cc_final: 0.7425 (m-30) REVERT: E 63 GLU cc_start: 0.7922 (tp30) cc_final: 0.7468 (tt0) REVERT: E 96 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: B 176 THR cc_start: 0.7078 (p) cc_final: 0.6667 (t) REVERT: B 179 GLN cc_start: 0.7527 (tp-100) cc_final: 0.6975 (tp40) REVERT: B 286 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7568 (mmt-90) REVERT: H 63 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.4857 (mttt) REVERT: H 247 MET cc_start: 0.6972 (mmm) cc_final: 0.6733 (mtm) REVERT: H 526 GLU cc_start: 0.6647 (mp0) cc_final: 0.5979 (tp30) REVERT: H 535 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6193 (mm-30) REVERT: A 78 MET cc_start: 0.5014 (mtm) cc_final: 0.4484 (mtt) REVERT: A 125 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.4095 (ppp80) REVERT: A 186 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.3957 (tp) REVERT: J 89 LEU cc_start: 0.1668 (OUTLIER) cc_final: 0.1454 (tm) REVERT: I 279 LEU cc_start: 0.6017 (mp) cc_final: 0.5785 (mt) outliers start: 73 outliers final: 42 residues processed: 337 average time/residue: 0.4352 time to fit residues: 232.7522 Evaluate side-chains 293 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 321 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 94 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 245 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 271 optimal weight: 0.0270 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN D 104 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.211251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.155821 restraints weight = 38252.897| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.55 r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30543 Z= 0.132 Angle : 0.613 8.024 41898 Z= 0.323 Chirality : 0.043 0.201 4631 Planarity : 0.005 0.061 5001 Dihedral : 16.315 175.799 5082 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 2.58 % Allowed : 13.39 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -2.70 (0.14), residues: 3369 helix: -1.35 (0.17), residues: 951 sheet: -0.31 (0.23), residues: 505 loop : -2.55 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 143 HIS 0.008 0.001 HIS E 315 PHE 0.016 0.001 PHE G 89 TYR 0.015 0.001 TYR C 275 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 714) hydrogen bonds : angle 4.81248 ( 1920) covalent geometry : bond 0.00300 (30543) covalent geometry : angle 0.61256 (41898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 250 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 99 GLN cc_start: 0.7815 (pm20) cc_final: 0.7418 (mm-40) REVERT: G 123 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6436 (tt) REVERT: G 192 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7340 (tp30) REVERT: G 202 ASP cc_start: 0.7246 (m-30) cc_final: 0.6959 (m-30) REVERT: G 229 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7116 (tt0) REVERT: G 334 MET cc_start: 0.7470 (mtp) cc_final: 0.7043 (mtp) REVERT: G 349 HIS cc_start: 0.6754 (t70) cc_final: 0.6316 (t-170) REVERT: F 180 ASP cc_start: 0.8047 (m-30) cc_final: 0.7647 (m-30) REVERT: E 63 GLU cc_start: 0.8068 (tp30) cc_final: 0.7608 (tt0) REVERT: E 96 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: B 176 THR cc_start: 0.7127 (p) cc_final: 0.6704 (t) REVERT: B 179 GLN cc_start: 0.7553 (tp-100) cc_final: 0.7015 (tp40) REVERT: B 286 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7725 (mmt-90) REVERT: H 63 LYS cc_start: 0.5630 (OUTLIER) cc_final: 0.4646 (mttt) REVERT: H 70 LYS cc_start: 0.7042 (tmtt) cc_final: 0.6623 (tptm) REVERT: H 247 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6933 (mtm) REVERT: H 526 GLU cc_start: 0.6678 (mp0) cc_final: 0.5959 (tp30) REVERT: H 535 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6287 (mm-30) REVERT: A 78 MET cc_start: 0.4965 (mtm) cc_final: 0.4301 (mtt) REVERT: A 125 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.4039 (ppp80) REVERT: A 186 LEU cc_start: 0.4311 (OUTLIER) cc_final: 0.3984 (tp) REVERT: J 89 LEU cc_start: 0.1674 (OUTLIER) cc_final: 0.1462 (tm) outliers start: 78 outliers final: 59 residues processed: 313 average time/residue: 0.4590 time to fit residues: 230.2777 Evaluate side-chains 309 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 543 TYR Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 198 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN D 104 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.209395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152144 restraints weight = 37903.455| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.70 r_work: 0.3219 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30543 Z= 0.171 Angle : 0.661 9.119 41898 Z= 0.348 Chirality : 0.045 0.201 4631 Planarity : 0.005 0.061 5001 Dihedral : 16.375 175.329 5082 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.74 % Allowed : 13.55 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -2.77 (0.14), residues: 3369 helix: -1.40 (0.16), residues: 952 sheet: -0.45 (0.23), residues: 517 loop : -2.58 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 143 HIS 0.006 0.001 HIS D 335 PHE 0.018 0.001 PHE G 89 TYR 0.016 0.002 TYR J 62 ARG 0.006 0.000 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 714) hydrogen bonds : angle 4.94265 ( 1920) covalent geometry : bond 0.00399 (30543) covalent geometry : angle 0.66070 (41898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 248 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 99 GLN cc_start: 0.7870 (pm20) cc_final: 0.7412 (mm-40) REVERT: G 112 LEU cc_start: 0.8112 (mm) cc_final: 0.7638 (mm) REVERT: G 123 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6292 (tt) REVERT: G 192 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7330 (tp30) REVERT: G 202 ASP cc_start: 0.7322 (m-30) cc_final: 0.7071 (m-30) REVERT: G 220 MET cc_start: 0.7277 (mpp) cc_final: 0.6782 (mpp) REVERT: G 229 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7140 (tt0) REVERT: G 334 MET cc_start: 0.7561 (mtp) cc_final: 0.7134 (mtp) REVERT: G 349 HIS cc_start: 0.6758 (t70) cc_final: 0.6318 (t-170) REVERT: F 180 ASP cc_start: 0.8067 (m-30) cc_final: 0.7663 (m-30) REVERT: E 63 GLU cc_start: 0.8028 (tp30) cc_final: 0.7600 (tt0) REVERT: E 96 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: E 104 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8476 (t0) REVERT: E 164 GLU cc_start: 0.6496 (pm20) cc_final: 0.6158 (mp0) REVERT: C 165 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7435 (mtmm) REVERT: B 176 THR cc_start: 0.7146 (p) cc_final: 0.6746 (t) REVERT: B 286 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7793 (mpt180) REVERT: H 63 LYS cc_start: 0.5120 (OUTLIER) cc_final: 0.4449 (mttt) REVERT: H 70 LYS cc_start: 0.7083 (tmtt) cc_final: 0.6597 (tptm) REVERT: H 526 GLU cc_start: 0.6645 (mp0) cc_final: 0.5927 (tp30) REVERT: H 535 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6413 (mm-30) REVERT: A 78 MET cc_start: 0.4859 (mtm) cc_final: 0.4314 (mtt) REVERT: A 125 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.3988 (ppp80) REVERT: J 89 LEU cc_start: 0.1602 (OUTLIER) cc_final: 0.1390 (tm) outliers start: 83 outliers final: 64 residues processed: 315 average time/residue: 0.4155 time to fit residues: 210.5750 Evaluate side-chains 315 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 292 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 543 TYR Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 293 optimal weight: 50.0000 chunk 159 optimal weight: 0.0870 overall best weight: 2.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN D 104 ASN C 162 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.207783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151608 restraints weight = 38024.599| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.68 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30543 Z= 0.216 Angle : 0.712 10.091 41898 Z= 0.375 Chirality : 0.047 0.206 4631 Planarity : 0.006 0.070 5001 Dihedral : 16.484 175.211 5082 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.58 % Allowed : 13.98 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % Twisted General : 0.00 % 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: -2.88 (0.14), residues: 3369 helix: -1.48 (0.16), residues: 946 sheet: -0.55 (0.23), residues: 513 loop : -2.64 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 143 HIS 0.007 0.001 HIS H 272 PHE 0.022 0.002 PHE E 347 TYR 0.019 0.002 TYR E 275 ARG 0.009 0.001 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 714) hydrogen bonds : angle 5.04155 ( 1920) covalent geometry : bond 0.00512 (30543) covalent geometry : angle 0.71223 (41898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 252 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 112 LEU cc_start: 0.8117 (mm) cc_final: 0.7628 (mm) REVERT: G 123 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6333 (tt) REVERT: G 192 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7145 (tp30) REVERT: G 202 ASP cc_start: 0.7278 (m-30) cc_final: 0.7070 (m-30) REVERT: G 220 MET cc_start: 0.7075 (mpp) cc_final: 0.6575 (mpp) REVERT: G 229 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7067 (tt0) REVERT: G 334 MET cc_start: 0.7444 (mtp) cc_final: 0.7031 (mtp) REVERT: G 349 HIS cc_start: 0.6645 (t70) cc_final: 0.6273 (t-170) REVERT: F 180 ASP cc_start: 0.7849 (m-30) cc_final: 0.7377 (m-30) REVERT: E 63 GLU cc_start: 0.7905 (tp30) cc_final: 0.7501 (tt0) REVERT: E 96 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: E 104 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (t0) REVERT: C 165 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7289 (mtmm) REVERT: B 176 THR cc_start: 0.7075 (p) cc_final: 0.6679 (t) REVERT: B 286 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7655 (mpt180) REVERT: H 63 LYS cc_start: 0.4924 (OUTLIER) cc_final: 0.4240 (mttt) REVERT: H 526 GLU cc_start: 0.6527 (mp0) cc_final: 0.5970 (tp30) REVERT: H 535 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6264 (mm-30) REVERT: A 78 MET cc_start: 0.4982 (mtm) cc_final: 0.4468 (mtt) REVERT: A 125 ARG cc_start: 0.4979 (OUTLIER) cc_final: 0.3969 (ppp80) REVERT: A 187 SER cc_start: 0.4500 (m) cc_final: 0.3940 (t) REVERT: J 89 LEU cc_start: 0.1714 (OUTLIER) cc_final: 0.1509 (tm) outliers start: 78 outliers final: 68 residues processed: 314 average time/residue: 0.4105 time to fit residues: 208.3618 Evaluate side-chains 321 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 292 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 543 TYR Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 187 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 ASN J 368 HIS I 368 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.213443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156624 restraints weight = 38314.541| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.91 r_work: 0.3277 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30543 Z= 0.107 Angle : 0.583 7.984 41898 Z= 0.307 Chirality : 0.042 0.209 4631 Planarity : 0.005 0.060 5001 Dihedral : 16.302 175.611 5082 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.75 % Allowed : 15.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.52 (0.14), residues: 3369 helix: -1.10 (0.17), residues: 950 sheet: -0.32 (0.23), residues: 523 loop : -2.48 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 143 HIS 0.007 0.001 HIS E 315 PHE 0.014 0.001 PHE G 89 TYR 0.020 0.001 TYR C 275 ARG 0.007 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 714) hydrogen bonds : angle 4.70573 ( 1920) covalent geometry : bond 0.00232 (30543) covalent geometry : angle 0.58306 (41898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18624.50 seconds wall clock time: 325 minutes 50.89 seconds (19550.89 seconds total)