Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 09:48:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/04_2023/7trc_26085.pdb" } resolution = 3.3 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= 0.000 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 92 5.49 5 S 85 5.16 5 C 9016 2.51 5 N 2609 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 511": "OE1" <-> "OE2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14747 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2572 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 21, 'TRANS': 308} Chain breaks: 3 Chain: "G" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2703 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "B" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1973 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 35} Link IDs: {'rna2p': 15, 'rna3p': 76} Chain breaks: 2 Chain: "H" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 118} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "E" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 118} Chain: "C" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2830 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 14, 'TRANS': 342} Chain breaks: 1 Time building chain proxies: 8.66, per 1000 atoms: 0.59 Number of scatterers: 14747 At special positions: 0 Unit cell: (156.2, 116.6, 121, 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 85 16.00 P 92 15.00 O 2945 8.00 N 2609 7.00 C 9016 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: 6.74 Conformation dependent library (CDL) restraints added in 2.2 seconds 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 21 sheets defined 25.9% alpha, 23.9% beta 22 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'K' and resid 162 through 167 removed outlier: 3.521A pdb=" N THR K 166 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN K 167 " --> pdb=" O PHE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 242 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.691A pdb=" N ILE G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.789A pdb=" N VAL G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 142 removed outlier: 4.587A pdb=" N ARG G 141 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.595A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 175 removed outlier: 3.804A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 238 removed outlier: 4.053A pdb=" N VAL G 231 " --> pdb=" O ARG G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 277 removed outlier: 3.577A pdb=" N VAL G 266 " --> pdb=" O THR G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 290 through 293 Processing helix chain 'G' and resid 302 through 312 removed outlier: 3.657A pdb=" N VAL G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.846A pdb=" N ARG H 156 " --> pdb=" O PRO H 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 56 Processing helix chain 'I' and resid 63 through 73 removed outlier: 3.641A pdb=" N ASN I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS I 73 " --> pdb=" O LYS I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.800A pdb=" N VAL I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 100 removed outlier: 3.779A pdb=" N GLU I 99 " --> pdb=" O PRO I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 135 through 148 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.663A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.784A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.852A pdb=" N VAL E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR E 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 93 through 101 removed outlier: 4.829A pdb=" N GLU E 99 " --> pdb=" O PRO E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.679A pdb=" N ARG C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.593A pdb=" N THR C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.764A pdb=" N THR C 140 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 141 " --> pdb=" O ARG C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 166 through 176 removed outlier: 4.089A pdb=" N SER C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.696A pdb=" N VAL C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 267 " --> pdb=" O MET C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 290 through 294 removed outlier: 4.211A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 311 removed outlier: 4.329A pdb=" N ASN C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 383 through 396 removed outlier: 3.629A pdb=" N LYS C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 155 through 160 removed outlier: 5.836A pdb=" N PHE K 156 " --> pdb=" O LEU K 510 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU K 510 " --> pdb=" O PHE K 156 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER K 158 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER K 468 " --> pdb=" O ALA K 477 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY K 466 " --> pdb=" O ALA K 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 172 through 177 removed outlier: 5.299A pdb=" N ASN K 187 " --> pdb=" O LYS K 173 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS K 175 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU K 185 " --> pdb=" O CYS K 175 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP K 177 " --> pdb=" O CYS K 183 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS K 183 " --> pdb=" O TRP K 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR K 196 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE K 195 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU K 218 " --> pdb=" O ILE K 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 228 through 231 removed outlier: 4.006A pdb=" N ASP K 228 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE K 254 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER K 267 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE K 256 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 282 through 285 removed outlier: 3.706A pdb=" N SER K 282 " --> pdb=" O GLY K 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'K' and resid 328 through 334 removed outlier: 6.544A pdb=" N GLY K 343 " --> pdb=" O SER K 329 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE K 331 " --> pdb=" O ALA K 341 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA K 341 " --> pdb=" O ILE K 331 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE K 333 " --> pdb=" O LEU K 339 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU K 339 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU K 351 " --> pdb=" O ALA K 361 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA K 361 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA K 353 " --> pdb=" O PRO K 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 373 through 375 removed outlier: 3.973A pdb=" N PHE K 382 " --> pdb=" O TRP K 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 419 through 421 removed outlier: 3.610A pdb=" N LEU K 428 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU K 455 " --> pdb=" O VAL K 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.703A pdb=" N VAL G 300 " --> pdb=" O LEU G 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 118 through 120 removed outlier: 6.820A pdb=" N THR G 129 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE G 156 " --> pdb=" O GLN G 244 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU G 246 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL G 154 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG G 248 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU G 152 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 213 " --> pdb=" O TYR G 207 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR G 207 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE G 215 " --> pdb=" O ILE G 205 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG G 195 " --> pdb=" O GLN G 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.903A pdb=" N GLY G 130 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 132 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY G 90 " --> pdb=" O ILE G 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 250 through 251 Processing sheet with id=AB4, first strand: chain 'G' and resid 315 through 316 removed outlier: 6.850A pdb=" N ILE G 315 " --> pdb=" O VAL G 363 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET G 345 " --> pdb=" O LYS G 367 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL G 369 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE G 343 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS G 344 " --> pdb=" O VAL G 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB6, first strand: chain 'H' and resid 71 through 79 removed outlier: 5.472A pdb=" N PHE H 76 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS H 87 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE H 123 " --> pdb=" O CYS H 88 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL H 102 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 74 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE H 146 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 72 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.715A pdb=" N MET I 79 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE I 108 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU I 81 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 287 through 288 removed outlier: 4.173A pdb=" N GLY C 130 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR C 129 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ARG C 250 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 131 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N MET C 243 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG C 158 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 245 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 152 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 201 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY D 118 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 112 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE D 123 " --> pdb=" O CYS D 88 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D 102 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AC1, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.630A pdb=" N MET E 79 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE E 108 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU E 81 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.773A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 335 " --> pdb=" O CYS C 344 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS C 344 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE C 343 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL C 369 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET C 345 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE C 315 " --> pdb=" O VAL C 363 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 7.00 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: 3905 1.33 - 1.45: 2985 1.45 - 1.57: 8054 1.57 - 1.69: 181 1.69 - 1.81: 124 Bond restraints: 15249 Sorted by residual: bond pdb=" CA ASP G 359 " pdb=" C ASP G 359 " ideal model delta sigma weight residual 1.522 1.542 -0.020 1.31e-02 5.83e+03 2.38e+00 bond pdb=" CA ARG I 101 " pdb=" C ARG I 101 " ideal model delta sigma weight residual 1.521 1.539 -0.017 1.31e-02 5.83e+03 1.74e+00 bond pdb=" N ARG C 195 " pdb=" CA ARG C 195 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" C GLU H 92 " pdb=" O GLU H 92 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.00e-02 1.00e+04 1.41e+00 bond pdb=" CA LYS C 127 " pdb=" C LYS C 127 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.29e-02 6.01e+03 1.19e+00 ... (remaining 15244 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 849 106.03 - 113.02: 8325 113.02 - 120.02: 5240 120.02 - 127.02: 6280 127.02 - 134.01: 359 Bond angle restraints: 21053 Sorted by residual: angle pdb=" N PHE H 138 " pdb=" CA PHE H 138 " pdb=" C PHE H 138 " ideal model delta sigma weight residual 110.28 116.67 -6.39 1.48e+00 4.57e-01 1.86e+01 angle pdb=" N LEU H 141 " pdb=" CA LEU H 141 " pdb=" C LEU H 141 " ideal model delta sigma weight residual 109.07 102.44 6.63 1.61e+00 3.86e-01 1.69e+01 angle pdb=" N ILE C 226 " pdb=" CA ILE C 226 " pdb=" C ILE C 226 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" C GLN H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta sigma weight residual 122.33 115.91 6.42 1.68e+00 3.54e-01 1.46e+01 angle pdb=" N LYS D 107 " pdb=" CA LYS D 107 " pdb=" CB LYS D 107 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 ... (remaining 21048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 8851 35.19 - 70.39: 197 70.39 - 105.58: 23 105.58 - 140.77: 2 140.77 - 175.96: 1 Dihedral angle restraints: 9074 sinusoidal: 4426 harmonic: 4648 Sorted by residual: dihedral pdb=" O4' U B 411 " pdb=" C1' U B 411 " pdb=" N1 U B 411 " pdb=" C2 U B 411 " ideal model delta sinusoidal sigma weight residual -128.00 47.96 -175.96 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ILE G 136 " pdb=" C ILE G 136 " pdb=" N GLU G 137 " pdb=" CA GLU G 137 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" O4' A B 374 " pdb=" C1' A B 374 " pdb=" N9 A B 374 " pdb=" C4 A B 374 " ideal model delta sinusoidal sigma weight residual 68.00 146.51 -78.51 1 1.70e+01 3.46e-03 2.66e+01 ... (remaining 9071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1915 0.044 - 0.089: 354 0.089 - 0.133: 140 0.133 - 0.177: 8 0.177 - 0.222: 1 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA PHE H 138 " pdb=" N PHE H 138 " pdb=" C PHE H 138 " pdb=" CB PHE H 138 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP G 359 " pdb=" N ASP G 359 " pdb=" C ASP G 359 " pdb=" CB ASP G 359 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA LYS E 69 " pdb=" N LYS E 69 " pdb=" C LYS E 69 " pdb=" CB LYS E 69 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2415 not shown) Planarity restraints: 2338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 21 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO J 22 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 22 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 22 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 135 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C ALA H 135 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA H 135 " 0.014 2.00e-02 2.50e+03 pdb=" N SER H 136 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 52 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO G 53 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.027 5.00e-02 4.00e+02 ... (remaining 2335 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 379 2.68 - 3.23: 13294 3.23 - 3.79: 21876 3.79 - 4.34: 30858 4.34 - 4.90: 49719 Nonbonded interactions: 116126 Sorted by model distance: nonbonded pdb=" O2' C B 379 " pdb=" O4' G B 380 " model vdw 2.121 2.440 nonbonded pdb=" OH TYR G 69 " pdb=" O ILE C 38 " model vdw 2.209 2.440 nonbonded pdb=" O THR K 371 " pdb=" NH1 ARG K 416 " model vdw 2.236 2.520 nonbonded pdb=" O LYS C 57 " pdb=" NH1 ARG C 298 " model vdw 2.272 2.520 nonbonded pdb=" O2' G B 370 " pdb=" N7 A B 372 " model vdw 2.277 2.520 ... (remaining 116121 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 'C' and resid 48 through 392) selection = (chain 'G' and (resid 48 through 185 or resid 192 through 392)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 68 through 158) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.510 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 45.600 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.003 0.037 15249 Z= 0.190 Angle : 0.641 8.326 21053 Z= 0.355 Chirality : 0.040 0.222 2418 Planarity : 0.005 0.058 2338 Dihedral : 14.829 175.963 6076 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.82 (0.21), residues: 1571 helix: -0.24 (0.29), residues: 330 sheet: -1.62 (0.27), residues: 350 loop : -1.38 (0.20), residues: 891 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 1.655 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 274 average time/residue: 0.3417 time to fit residues: 127.6599 Evaluate side-chains 175 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 470 HIS G 77 ASN G 103 HIS G 244 GLN H 78 HIS ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN E 32 ASN E 68 GLN C 244 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15249 Z= 0.267 Angle : 0.662 8.897 21053 Z= 0.337 Chirality : 0.044 0.211 2418 Planarity : 0.005 0.057 2338 Dihedral : 11.568 172.350 2851 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.64 (0.21), residues: 1571 helix: -0.10 (0.29), residues: 339 sheet: -1.41 (0.27), residues: 357 loop : -1.32 (0.21), residues: 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.634 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 19 residues processed: 194 average time/residue: 0.3540 time to fit residues: 95.5564 Evaluate side-chains 176 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1639 time to fit residues: 7.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 ASN D 93 ASN E 25 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 15249 Z= 0.315 Angle : 0.677 7.832 21053 Z= 0.346 Chirality : 0.045 0.240 2418 Planarity : 0.005 0.058 2338 Dihedral : 11.667 170.684 2851 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1571 helix: -0.16 (0.29), residues: 340 sheet: -1.20 (0.28), residues: 356 loop : -1.44 (0.21), residues: 875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.668 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 179 average time/residue: 0.3345 time to fit residues: 83.5427 Evaluate side-chains 170 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1387 time to fit residues: 5.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN I 32 ASN E 25 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15249 Z= 0.167 Angle : 0.567 8.646 21053 Z= 0.288 Chirality : 0.041 0.185 2418 Planarity : 0.005 0.056 2338 Dihedral : 11.352 173.104 2851 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.35 (0.21), residues: 1571 helix: 0.16 (0.29), residues: 344 sheet: -1.14 (0.28), residues: 359 loop : -1.20 (0.21), residues: 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.701 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 188 average time/residue: 0.3385 time to fit residues: 88.2442 Evaluate side-chains 170 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1312 time to fit residues: 4.1605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 482 GLN J 10 GLN J 31 HIS I 32 ASN F 4 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 15249 Z= 0.436 Angle : 0.758 10.987 21053 Z= 0.387 Chirality : 0.049 0.213 2418 Planarity : 0.006 0.058 2338 Dihedral : 11.901 168.542 2851 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1571 helix: -0.26 (0.28), residues: 341 sheet: -1.25 (0.28), residues: 357 loop : -1.52 (0.21), residues: 873 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.798 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 196 average time/residue: 0.3215 time to fit residues: 89.2357 Evaluate side-chains 189 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1346 time to fit residues: 6.7309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 159 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 ASN J 10 GLN I 32 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 15249 Z= 0.243 Angle : 0.632 9.558 21053 Z= 0.321 Chirality : 0.043 0.178 2418 Planarity : 0.005 0.057 2338 Dihedral : 11.566 171.289 2851 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.56 (0.21), residues: 1571 helix: -0.03 (0.29), residues: 341 sheet: -1.15 (0.28), residues: 352 loop : -1.38 (0.21), residues: 878 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.657 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 184 average time/residue: 0.3449 time to fit residues: 88.4125 Evaluate side-chains 175 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1502 time to fit residues: 5.3371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15249 Z= 0.165 Angle : 0.577 8.652 21053 Z= 0.290 Chirality : 0.041 0.160 2418 Planarity : 0.005 0.055 2338 Dihedral : 11.222 172.798 2851 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.28 (0.21), residues: 1571 helix: 0.35 (0.29), residues: 339 sheet: -1.06 (0.28), residues: 353 loop : -1.22 (0.21), residues: 879 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 1.771 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 187 average time/residue: 0.3293 time to fit residues: 86.6551 Evaluate side-chains 172 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1320 time to fit residues: 3.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 0.0070 chunk 144 optimal weight: 4.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 460 GLN J 10 GLN H 106 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15249 Z= 0.241 Angle : 0.621 8.896 21053 Z= 0.315 Chirality : 0.043 0.201 2418 Planarity : 0.005 0.052 2338 Dihedral : 11.307 171.398 2851 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.31 (0.21), residues: 1571 helix: 0.21 (0.29), residues: 341 sheet: -1.02 (0.28), residues: 347 loop : -1.22 (0.21), residues: 883 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.910 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 181 average time/residue: 0.3381 time to fit residues: 86.0493 Evaluate side-chains 172 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1481 time to fit residues: 4.8653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 0.0270 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN H 106 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.003 0.040 15249 Z= 0.161 Angle : 0.572 8.627 21053 Z= 0.287 Chirality : 0.040 0.172 2418 Planarity : 0.005 0.057 2338 Dihedral : 11.125 173.241 2851 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.14 (0.22), residues: 1571 helix: 0.49 (0.29), residues: 338 sheet: -1.04 (0.28), residues: 357 loop : -1.11 (0.21), residues: 876 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 1.745 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 173 average time/residue: 0.3482 time to fit residues: 85.0033 Evaluate side-chains 164 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1744 time to fit residues: 2.9953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 0.0030 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 10 GLN H 106 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 15249 Z= 0.339 Angle : 0.692 9.712 21053 Z= 0.351 Chirality : 0.045 0.202 2418 Planarity : 0.005 0.058 2338 Dihedral : 11.487 169.965 2851 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1571 helix: 0.05 (0.29), residues: 341 sheet: -1.07 (0.28), residues: 347 loop : -1.31 (0.21), residues: 883 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 1.849 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 169 average time/residue: 0.3522 time to fit residues: 82.8105 Evaluate side-chains 165 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2527 time to fit residues: 4.3190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.0980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN H 106 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128584 restraints weight = 19320.522| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.53 r_work: 0.3590 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 15249 Z= 0.152 Angle : 0.579 11.296 21053 Z= 0.292 Chirality : 0.040 0.250 2418 Planarity : 0.004 0.052 2338 Dihedral : 11.151 173.255 2851 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % 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: -1.17 (0.21), residues: 1571 helix: 0.45 (0.29), residues: 339 sheet: -1.06 (0.28), residues: 360 loop : -1.12 (0.21), residues: 872 =============================================================================== Job complete usr+sys time: 3166.78 seconds wall clock time: 58 minutes 21.42 seconds (3501.42 seconds total)