Starting phenix.real_space_refine (version: dev) on Sun May 15 09:38:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqv_21358/05_2022/6vqv_21358.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 sd= 0.089 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ARG 68": "NH1" <-> "NH2" Residue "K ARG 73": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Residue "K ARG 147": "NH1" <-> "NH2" Residue "K ARG 160": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 24676 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3378 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "D" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2410 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 23, 'TRANS': 282} Chain breaks: 1 Chain: "E" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2204 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'CIS': 1, 'TRANS': 273} Chain breaks: 2 Chain: "F" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2541 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "G" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2532 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2532 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "J" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2611 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "K" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 15, 'TRANS': 171} Chain: "L" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1275 Classifications: {'RNA': 60} Modifications used: {'rna3p_pyr': 19, 'rna2p_pur': 9, 'rna3p_pur': 20, 'rna2p_pyr': 12} Link IDs: {'rna3p': 39, 'rna2p': 20} Time building chain proxies: 13.73, per 1000 atoms: 0.56 Number of scatterers: 24676 At special positions: 0 Unit cell: (151.45, 141.05, 150.15, 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 33 16.00 P 60 15.00 O 4801 8.00 N 4514 7.00 C 15268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 24.8% alpha, 21.6% beta 0 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.807A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 212 through 224 removed outlier: 3.584A pdb=" N ALA C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 342 removed outlier: 4.286A pdb=" N ARG C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 386 removed outlier: 4.006A pdb=" N GLU C 386 " --> pdb=" O TRP C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 386' Processing helix chain 'C' and resid 387 through 397 removed outlier: 3.743A pdb=" N TRP C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 removed outlier: 3.580A pdb=" N SER C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 418 " --> pdb=" O TRP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'D' and resid 33 through 46 removed outlier: 3.992A pdb=" N PHE D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.793A pdb=" N LEU D 118 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 removed outlier: 3.571A pdb=" N ILE D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 189 through 196 removed outlier: 4.153A pdb=" N LEU D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 212 removed outlier: 3.543A pdb=" N LEU D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.749A pdb=" N LEU D 302 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 Processing helix chain 'E' and resid 149 through 162 removed outlier: 3.560A pdb=" N ARG E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 162 " --> pdb=" O HIS E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 223 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 321 through 331 removed outlier: 3.684A pdb=" N TRP E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 351 Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.856A pdb=" N ASP F 86 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.662A pdb=" N ARG F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 162 removed outlier: 3.629A pdb=" N HIS F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 222 removed outlier: 3.705A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 337 through 351 removed outlier: 3.971A pdb=" N HIS F 342 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 351 " --> pdb=" O ASN F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.794A pdb=" N ARG G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 4.090A pdb=" N ARG G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 160 " --> pdb=" O TYR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 200 Processing helix chain 'G' and resid 209 through 222 removed outlier: 3.658A pdb=" N LEU G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 321 through 331 removed outlier: 3.622A pdb=" N TRP G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 removed outlier: 3.632A pdb=" N HIS G 342 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 removed outlier: 3.778A pdb=" N ARG H 51 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP H 52 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER H 54 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 3.852A pdb=" N LEU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.579A pdb=" N ASP H 146 " --> pdb=" O THR H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.514A pdb=" N HIS H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.589A pdb=" N LEU H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 281 Processing helix chain 'H' and resid 321 through 331 removed outlier: 3.699A pdb=" N ASN H 328 " --> pdb=" O THR H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 removed outlier: 3.627A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 57 removed outlier: 3.556A pdb=" N ALA I 53 " --> pdb=" O GLN I 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER I 54 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN I 55 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU I 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP I 57 " --> pdb=" O SER I 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 50 through 57' Processing helix chain 'I' and resid 81 through 91 removed outlier: 4.033A pdb=" N ALA I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 147 Processing helix chain 'I' and resid 149 through 162 Processing helix chain 'I' and resid 209 through 222 removed outlier: 3.818A pdb=" N LEU I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 281 Processing helix chain 'I' and resid 321 through 331 Processing helix chain 'I' and resid 337 through 351 removed outlier: 3.733A pdb=" N HIS I 342 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY I 351 " --> pdb=" O ASN I 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 removed outlier: 4.460A pdb=" N GLU J 56 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP J 57 " --> pdb=" O SER J 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 53 through 57' Processing helix chain 'J' and resid 81 through 87 Processing helix chain 'J' and resid 129 through 145 removed outlier: 3.525A pdb=" N GLN J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 162 removed outlier: 3.625A pdb=" N ARG J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 160 " --> pdb=" O TYR J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 223 removed outlier: 3.955A pdb=" N ALA J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 213 " --> pdb=" O GLU J 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 321 through 331 removed outlier: 4.207A pdb=" N ASP J 327 " --> pdb=" O TYR J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 350 removed outlier: 3.520A pdb=" N TYR J 343 " --> pdb=" O GLU J 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 69 removed outlier: 4.216A pdb=" N ARG K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 73 removed outlier: 4.396A pdb=" N ARG K 73 " --> pdb=" O LEU K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.594A pdb=" N TYR A 5 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 45 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR A 57 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 47 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.595A pdb=" N TYR B 5 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 45 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR B 57 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 47 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 181 removed outlier: 5.098A pdb=" N ILE D 61 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N SER D 188 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 13.520A pdb=" N VAL D 59 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 59 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY D 112 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE D 61 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 110 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS D 63 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 108 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 65 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D 103 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN D 18 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 105 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 16 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 107 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG D 14 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 11 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 157 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.277A pdb=" N SER D 16 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG D 14 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 107 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 16 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 105 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN D 18 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D 103 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 65 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 108 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS D 63 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 110 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE D 61 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY D 112 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 59 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 13.520A pdb=" N VAL D 59 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N SER D 188 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE D 61 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE D 279 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA D 257 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU D 281 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR D 255 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU D 283 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP D 247 " --> pdb=" O TRP D 289 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA D 253 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP D 316 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 30 removed outlier: 4.681A pdb=" N PHE D 81 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LYS C 242 " --> pdb=" O PHE D 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AA9, first strand: chain 'E' and resid 31 through 32 Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.558A pdb=" N ALA E 235 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.555A pdb=" N ARG E 190 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 235 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.715A pdb=" N ALA F 126 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 30 " --> pdb=" O PHE F 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 37 through 38 removed outlier: 4.197A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU F 228 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 180 " --> pdb=" O TRP F 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG F 190 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 63 through 68 removed outlier: 3.516A pdb=" N VAL F 99 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 67 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA F 100 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 247 through 248 removed outlier: 4.559A pdb=" N THR F 263 " --> pdb=" O GLU F 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 305 through 306 removed outlier: 3.630A pdb=" N LYS F 311 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.341A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU G 228 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'G' and resid 62 through 69 removed outlier: 3.609A pdb=" N ASN G 93 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER G 261 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR G 96 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 263 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP G 98 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR G 263 " --> pdb=" O GLU G 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC6, first strand: chain 'G' and resid 305 through 306 removed outlier: 3.669A pdb=" N LYS G 311 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 126 through 127 Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.410A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA H 175 " --> pdb=" O ARG H 236 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 62 through 69 removed outlier: 4.591A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 247 through 248 removed outlier: 4.725A pdb=" N THR H 263 " --> pdb=" O GLU H 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 284 through 286 Processing sheet with id=AD4, first strand: chain 'H' and resid 305 through 306 Processing sheet with id=AD5, first strand: chain 'I' and resid 30 through 31 Processing sheet with id=AD6, first strand: chain 'I' and resid 37 through 38 removed outlier: 4.309A pdb=" N VAL I 227 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU I 228 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL I 176 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP I 195 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL I 178 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG I 193 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE I 180 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA I 191 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS I 182 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'I' and resid 62 through 68 removed outlier: 4.479A pdb=" N ALA I 100 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 62 through 68 removed outlier: 7.374A pdb=" N SER I 261 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR I 96 " --> pdb=" O SER I 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 305 through 306 removed outlier: 3.612A pdb=" N LYS I 311 " --> pdb=" O VAL I 306 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 126 through 127 Processing sheet with id=AE3, first strand: chain 'J' and resid 37 through 38 removed outlier: 4.530A pdb=" N LEU J 228 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA J 175 " --> pdb=" O ARG J 236 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 188 through 191 removed outlier: 4.122A pdb=" N ARG J 190 " --> pdb=" O HIS J 182 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA J 175 " --> pdb=" O ARG J 236 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU J 228 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 62 through 69 removed outlier: 4.468A pdb=" N ALA J 100 " --> pdb=" O VAL J 243 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4059 1.25 - 1.39: 6239 1.39 - 1.53: 13844 1.53 - 1.67: 1100 1.67 - 1.81: 50 Bond restraints: 25292 Sorted by residual: bond pdb=" C GLY G 46 " pdb=" O GLY G 46 " ideal model delta sigma weight residual 1.233 1.114 0.119 1.25e-02 6.40e+03 9.01e+01 bond pdb=" C SER G 44 " pdb=" O SER G 44 " ideal model delta sigma weight residual 1.234 1.121 0.113 1.24e-02 6.50e+03 8.26e+01 bond pdb=" CA PRO G 58 " pdb=" C PRO G 58 " ideal model delta sigma weight residual 1.521 1.410 0.111 1.24e-02 6.50e+03 8.02e+01 bond pdb=" C PRO G 58 " pdb=" O PRO G 58 " ideal model delta sigma weight residual 1.233 1.130 0.103 1.19e-02 7.06e+03 7.55e+01 bond pdb=" CA GLN G 50 " pdb=" C GLN G 50 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.56e+01 ... (remaining 25287 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.62: 611 104.62 - 113.13: 13638 113.13 - 121.64: 13896 121.64 - 130.16: 6227 130.16 - 138.67: 213 Bond angle restraints: 34585 Sorted by residual: angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 110.44 96.11 14.33 1.20e+00 6.94e-01 1.43e+02 angle pdb=" C TRP G 57 " pdb=" CA TRP G 57 " pdb=" CB TRP G 57 " ideal model delta sigma weight residual 109.15 124.94 -15.79 1.60e+00 3.91e-01 9.74e+01 angle pdb=" C TRP G 48 " pdb=" N ALA G 49 " pdb=" CA ALA G 49 " ideal model delta sigma weight residual 123.34 138.67 -15.33 1.80e+00 3.09e-01 7.25e+01 angle pdb=" CA GLU A 18 " pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.78e+01 angle pdb=" CA GLU B 18 " pdb=" CB GLU B 18 " pdb=" CG GLU B 18 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.77e+01 ... (remaining 34580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 14622 28.35 - 56.69: 421 56.69 - 85.04: 46 85.04 - 113.38: 3 113.38 - 141.73: 2 Dihedral angle restraints: 15094 sinusoidal: 6487 harmonic: 8607 Sorted by residual: dihedral pdb=" C4' C L 58 " pdb=" C3' C L 58 " pdb=" C2' C L 58 " pdb=" C1' C L 58 " ideal model delta sinusoidal sigma weight residual -35.00 32.81 -67.81 1 8.00e+00 1.56e-02 9.33e+01 dihedral pdb=" C5' C L 58 " pdb=" C4' C L 58 " pdb=" C3' C L 58 " pdb=" O3' C L 58 " ideal model delta sinusoidal sigma weight residual 147.00 79.71 67.29 1 8.00e+00 1.56e-02 9.21e+01 dihedral pdb=" N SER G 54 " pdb=" C SER G 54 " pdb=" CA SER G 54 " pdb=" CB SER G 54 " ideal model delta harmonic sigma weight residual 122.80 146.29 -23.49 0 2.50e+00 1.60e-01 8.83e+01 ... (remaining 15091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 3844 0.219 - 0.437: 19 0.437 - 0.656: 1 0.656 - 0.874: 0 0.874 - 1.093: 2 Chirality restraints: 3866 Sorted by residual: chirality pdb=" CA SER G 54 " pdb=" N SER G 54 " pdb=" C SER G 54 " pdb=" CB SER G 54 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CA TRP G 57 " pdb=" N TRP G 57 " pdb=" C TRP G 57 " pdb=" CB TRP G 57 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CA ALA G 49 " pdb=" N ALA G 49 " pdb=" C ALA G 49 " pdb=" CB ALA G 49 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 3863 not shown) Planarity restraints: 4337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 47 " -0.024 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ALA G 47 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA G 47 " -0.028 2.00e-02 2.50e+03 pdb=" N TRP G 48 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 329 " -0.029 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP F 329 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 329 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP F 329 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 329 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 329 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 329 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 268 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG E 268 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG E 268 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP E 269 " 0.022 2.00e-02 2.50e+03 ... (remaining 4334 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5206 2.78 - 3.31: 20588 3.31 - 3.84: 40650 3.84 - 4.37: 47886 4.37 - 4.90: 81096 Nonbonded interactions: 195426 Sorted by model distance: nonbonded pdb=" O2' U L 39 " pdb=" OP2 G L 41 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP C 107 " pdb=" OG SER C 252 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR E 323 " pdb=" O SER F 72 " model vdw 2.278 2.440 nonbonded pdb=" OD1 ASN A 12 " pdb=" OG SER A 15 " model vdw 2.288 2.440 nonbonded pdb=" OD1 ASN B 12 " pdb=" OG SER B 15 " model vdw 2.289 2.440 ... (remaining 195421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and resid 24 through 356) selection = (chain 'F' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'G' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'H' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'I' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 33 5.16 5 C 15268 2.51 5 N 4514 2.21 5 O 4801 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.360 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: 13.840 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.200 Process input model: 66.110 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.010 0.137 25292 Z= 0.624 Angle : 1.116 15.794 34585 Z= 0.627 Chirality : 0.064 1.093 3866 Planarity : 0.008 0.080 4337 Dihedral : 12.885 141.726 9530 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.63 % Favored : 91.31 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.98 (0.12), residues: 2956 helix: -3.33 (0.13), residues: 719 sheet: -0.46 (0.23), residues: 478 loop : -3.14 (0.11), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 360 time to evaluate : 2.822 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 5 residues processed: 380 average time/residue: 1.5504 time to fit residues: 666.5652 Evaluate side-chains 238 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 2.501 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.2459 time to fit residues: 6.4245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 270 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 HIS C 237 ASN C 250 ASN C 256 ASN C 283 HIS C 289 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN D 293 HIS E 128 ASN E 145 ASN E 158 HIS E 159 ASN E 328 ASN E 340 GLN F 128 ASN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 HIS G 50 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN H 342 HIS I 55 GLN I 95 GLN I 128 ASN I 226 HIS I 280 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN J 241 GLN K 29 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 25292 Z= 0.172 Angle : 0.620 14.809 34585 Z= 0.327 Chirality : 0.040 0.173 3866 Planarity : 0.005 0.060 4337 Dihedral : 10.331 123.147 4002 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -2.95 (0.14), residues: 2956 helix: -1.79 (0.17), residues: 718 sheet: 0.26 (0.24), residues: 465 loop : -2.81 (0.12), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 291 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 12 residues processed: 323 average time/residue: 1.3748 time to fit residues: 510.4778 Evaluate side-chains 244 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.5280 time to fit residues: 9.4514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 225 optimal weight: 0.0470 chunk 184 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 21 GLN C 203 HIS C 255 ASN C 283 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 82 ASN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN E 342 HIS ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN G 128 ASN G 138 GLN G 182 HIS G 185 GLN G 347 ASN H 95 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS K 154 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.157 25292 Z= 0.370 Angle : 0.720 16.120 34585 Z= 0.376 Chirality : 0.045 0.251 3866 Planarity : 0.006 0.114 4337 Dihedral : 10.405 129.371 4002 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.96 % Favored : 91.00 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -2.58 (0.14), residues: 2956 helix: -1.36 (0.18), residues: 730 sheet: 0.38 (0.24), residues: 487 loop : -2.64 (0.13), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 249 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 31 residues processed: 303 average time/residue: 1.3926 time to fit residues: 486.6710 Evaluate side-chains 261 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 13 average time/residue: 0.4932 time to fit residues: 12.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 142 optimal weight: 0.1980 chunk 257 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN E 145 ASN F 159 ASN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 138 GLN G 280 ASN G 347 ASN H 95 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 25292 Z= 0.220 Angle : 0.598 9.714 34585 Z= 0.316 Chirality : 0.041 0.252 3866 Planarity : 0.005 0.079 4337 Dihedral : 9.996 126.068 4002 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -2.21 (0.15), residues: 2956 helix: -0.77 (0.18), residues: 732 sheet: 0.59 (0.24), residues: 485 loop : -2.54 (0.13), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 245 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 38 residues processed: 300 average time/residue: 1.3665 time to fit residues: 475.3117 Evaluate side-chains 267 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 27 residues processed: 14 average time/residue: 0.6499 time to fit residues: 15.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 0.1980 chunk 163 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 214 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 25292 Z= 0.253 Angle : 0.617 13.985 34585 Z= 0.325 Chirality : 0.041 0.262 3866 Planarity : 0.005 0.107 4337 Dihedral : 9.868 126.777 4002 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.99 (0.15), residues: 2956 helix: -0.46 (0.19), residues: 734 sheet: 0.65 (0.24), residues: 492 loop : -2.45 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 237 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 40 residues processed: 292 average time/residue: 1.2733 time to fit residues: 433.3726 Evaluate side-chains 261 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 221 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 28 residues processed: 14 average time/residue: 0.6078 time to fit residues: 14.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 95 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 38 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 138 GLN G 159 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.201 25292 Z= 0.464 Angle : 0.749 14.082 34585 Z= 0.394 Chirality : 0.046 0.305 3866 Planarity : 0.006 0.096 4337 Dihedral : 10.296 131.190 4002 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -2.20 (0.15), residues: 2956 helix: -0.72 (0.18), residues: 731 sheet: 0.57 (0.24), residues: 468 loop : -2.51 (0.14), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 230 time to evaluate : 2.852 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 45 residues processed: 286 average time/residue: 1.3949 time to fit residues: 462.5174 Evaluate side-chains 262 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 15 average time/residue: 0.8363 time to fit residues: 19.6470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS C 250 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 185 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.317 25292 Z= 0.274 Angle : 0.639 22.539 34585 Z= 0.344 Chirality : 0.041 0.287 3866 Planarity : 0.005 0.081 4337 Dihedral : 9.850 126.316 4002 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.87 (0.15), residues: 2956 helix: -0.24 (0.19), residues: 733 sheet: 0.64 (0.24), residues: 471 loop : -2.37 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 239 time to evaluate : 2.716 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 45 residues processed: 295 average time/residue: 1.3148 time to fit residues: 452.0048 Evaluate side-chains 265 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 9 average time/residue: 0.5211 time to fit residues: 10.0378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 159 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.726 25292 Z= 0.543 Angle : 0.796 73.900 34585 Z= 0.392 Chirality : 0.048 0.319 3866 Planarity : 0.005 0.113 4337 Dihedral : 9.867 126.979 4002 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.90 (0.15), residues: 2956 helix: -0.37 (0.19), residues: 739 sheet: 0.70 (0.24), residues: 486 loop : -2.40 (0.14), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 3.122 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 46 residues processed: 270 average time/residue: 1.4201 time to fit residues: 446.4228 Evaluate side-chains 263 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 10 average time/residue: 0.6118 time to fit residues: 12.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.726 25292 Z= 0.544 Angle : 0.796 73.900 34585 Z= 0.392 Chirality : 0.048 0.319 3866 Planarity : 0.005 0.113 4337 Dihedral : 9.867 126.979 4002 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.90 (0.15), residues: 2956 helix: -0.37 (0.19), residues: 739 sheet: 0.70 (0.24), residues: 486 loop : -2.40 (0.14), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 2.849 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 38 residues processed: 253 average time/residue: 1.4536 time to fit residues: 425.2636 Evaluate side-chains 252 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 3.209 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 2 average time/residue: 0.4213 time to fit residues: 5.1492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.8980 chunk 283 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 196 optimal weight: 0.8980 chunk 296 optimal weight: 30.0000 chunk 273 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 24 optimal weight: 0.0370 chunk 182 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.726 25292 Z= 0.544 Angle : 0.796 73.900 34585 Z= 0.392 Chirality : 0.048 0.319 3866 Planarity : 0.005 0.113 4337 Dihedral : 9.867 126.979 4002 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.90 (0.15), residues: 2956 helix: -0.37 (0.19), residues: 739 sheet: 0.70 (0.24), residues: 486 loop : -2.40 (0.14), residues: 1731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 2.703 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 38 residues processed: 250 average time/residue: 1.4146 time to fit residues: 411.7680 Evaluate side-chains 252 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 2 average time/residue: 0.4162 time to fit residues: 5.2040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 203 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 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 = 0.4288 r_free = 0.4288 target = 0.186741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135490 restraints weight = 32820.990| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.23 r_work: 0.3654 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.3633 rms_B_bonded: 2.07 restraints_weight: 0.1250 r_work: 0.3621 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.3609 rms_B_bonded: 2.27 restraints_weight: 0.0312 r_work: 0.3596 rms_B_bonded: 2.42 restraints_weight: 0.0156 r_work: 0.3582 rms_B_bonded: 2.61 restraints_weight: 0.0078 r_work: 0.3567 rms_B_bonded: 2.84 restraints_weight: 0.0039 r_work: 0.3551 rms_B_bonded: 3.11 restraints_weight: 0.0020 r_work: 0.3533 rms_B_bonded: 3.43 restraints_weight: 0.0010 r_work: 0.3514 rms_B_bonded: 3.81 restraints_weight: 0.0005 r_work: 0.3494 rms_B_bonded: 4.24 restraints_weight: 0.0002 r_work: 0.3471 rms_B_bonded: 4.75 restraints_weight: 0.0001 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.726 25292 Z= 0.544 Angle : 0.796 73.900 34585 Z= 0.392 Chirality : 0.048 0.319 3866 Planarity : 0.005 0.113 4337 Dihedral : 9.867 126.979 4002 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.90 (0.15), residues: 2956 helix: -0.37 (0.19), residues: 739 sheet: 0.70 (0.24), residues: 486 loop : -2.40 (0.14), residues: 1731 =============================================================================== Job complete usr+sys time: 8124.76 seconds wall clock time: 145 minutes 36.13 seconds (8736.13 seconds total)