Starting phenix.real_space_refine on Sat Mar 16 13:10:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/03_2024/7trc_26085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/03_2024/7trc_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_26085/03_2024/7trc_26085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/03_2024/7trc_26085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/03_2024/7trc_26085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trc_26085/03_2024/7trc_26085.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.43, per 1000 atoms: 0.57 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: 6.11 Conformation dependent library (CDL) restraints added in 2.4 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: 5.48 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: 4.78 Time building geometry restraints manager: 6.40 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: 9020 35.19 - 70.39: 363 70.39 - 105.58: 54 105.58 - 140.77: 2 140.77 - 175.96: 1 Dihedral angle restraints: 9440 sinusoidal: 4792 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 9437 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: 4.900 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: 0.000 Extract box with map and model: 7.720 Check model and map are aligned: 0.210 Set scattering table: 0.110 Process input model: 44.310 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.070 ------------------------------------------------------------------------------- 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 : 17.825 175.963 6442 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 % Allowed : 0.56 % Favored : 99.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 177 HIS 0.006 0.001 HIS C 259 PHE 0.024 0.002 PHE C 59 TYR 0.014 0.001 TYR I 48 ARG 0.007 0.000 ARG H 156 *********************** 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 : 1.517 Fit side-chains revert: symmetry clash REVERT: K 263 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6832 (mm-30) REVERT: K 310 ARG cc_start: 0.7178 (ptm-80) cc_final: 0.6708 (tpt170) REVERT: K 391 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6467 (pt0) REVERT: G 103 HIS cc_start: 0.7317 (p90) cc_final: 0.7096 (p90) REVERT: G 362 ILE cc_start: 0.8336 (mp) cc_final: 0.8065 (mt) REVERT: J 12 ASP cc_start: 0.7841 (p0) cc_final: 0.7453 (t0) REVERT: H 108 GLU cc_start: 0.5449 (mm-30) cc_final: 0.5115 (tp30) REVERT: I 42 ARG cc_start: 0.7291 (ptp-110) cc_final: 0.7043 (mtp85) REVERT: I 45 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6708 (ptp-110) REVERT: I 62 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6690 (mtt90) REVERT: I 66 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 75 GLU cc_start: 0.6211 (mp0) cc_final: 0.5829 (pt0) REVERT: F 1 MET cc_start: 0.7070 (mmt) cc_final: 0.6812 (mmt) REVERT: E 36 GLN cc_start: 0.6776 (mp10) cc_final: 0.6552 (mp10) REVERT: E 62 ARG cc_start: 0.5281 (ttm170) cc_final: 0.4416 (ttp-170) REVERT: E 102 ASN cc_start: 0.7614 (t0) cc_final: 0.7405 (t0) outliers start: 3 outliers final: 0 residues processed: 274 average time/residue: 0.3291 time to fit residues: 123.0685 Evaluate side-chains 177 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.3586 ------------------------------------------------------------------------------- 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 244 GLN H 78 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15249 Z= 0.342 Angle : 0.718 9.305 21053 Z= 0.366 Chirality : 0.047 0.229 2418 Planarity : 0.006 0.058 2338 Dihedral : 18.140 170.867 3217 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.84 % Allowed : 10.31 % Favored : 87.85 % 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: -0.25 (0.29), residues: 338 sheet: -1.36 (0.27), residues: 356 loop : -1.47 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 380 HIS 0.008 0.001 HIS K 273 PHE 0.031 0.003 PHE C 59 TYR 0.023 0.002 TYR I 91 ARG 0.006 0.001 ARG H 156 *********************** 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 201 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: K 298 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.7011 (mtt180) REVERT: J 12 ASP cc_start: 0.7819 (p0) cc_final: 0.7407 (t0) REVERT: H 108 GLU cc_start: 0.5750 (mm-30) cc_final: 0.5347 (tp30) REVERT: I 62 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.6745 (mtt90) REVERT: I 66 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7884 (mm-30) REVERT: D 75 GLU cc_start: 0.6932 (mp0) cc_final: 0.6605 (pm20) REVERT: F 1 MET cc_start: 0.7366 (mmt) cc_final: 0.6908 (mmt) REVERT: E 62 ARG cc_start: 0.5207 (ttm170) cc_final: 0.4466 (ttp-170) REVERT: E 102 ASN cc_start: 0.7518 (t0) cc_final: 0.7245 (t0) outliers start: 26 outliers final: 23 residues processed: 196 average time/residue: 0.3292 time to fit residues: 89.0718 Evaluate side-chains 183 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 508 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 335 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 78 HIS I 32 ASN D 93 ASN E 25 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15249 Z= 0.328 Angle : 0.691 8.082 21053 Z= 0.352 Chirality : 0.046 0.231 2418 Planarity : 0.006 0.060 2338 Dihedral : 18.142 170.568 3217 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.97 % Allowed : 12.85 % Favored : 84.18 % 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: -1.77 (0.21), residues: 1571 helix: -0.26 (0.29), residues: 340 sheet: -1.26 (0.27), residues: 356 loop : -1.50 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 380 HIS 0.010 0.001 HIS H 78 PHE 0.023 0.003 PHE C 59 TYR 0.021 0.002 TYR I 91 ARG 0.004 0.001 ARG G 298 *********************** 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 209 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: G 254 MET cc_start: 0.8696 (mmm) cc_final: 0.8436 (mmp) REVERT: G 260 MET cc_start: 0.7291 (ttt) cc_final: 0.6993 (ttt) REVERT: J 12 ASP cc_start: 0.7948 (p0) cc_final: 0.7521 (t0) REVERT: H 108 GLU cc_start: 0.5376 (mm-30) cc_final: 0.4982 (tp30) REVERT: I 62 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6858 (mtt90) REVERT: D 75 GLU cc_start: 0.7264 (mp0) cc_final: 0.6879 (pm20) REVERT: D 93 ASN cc_start: 0.7256 (m110) cc_final: 0.6904 (p0) REVERT: F 1 MET cc_start: 0.7467 (mmt) cc_final: 0.6929 (mmt) REVERT: E 102 ASN cc_start: 0.7627 (t0) cc_final: 0.7337 (t0) outliers start: 42 outliers final: 30 residues processed: 197 average time/residue: 0.3302 time to fit residues: 90.5853 Evaluate side-chains 192 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 508 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 392 MET 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: 0.9980 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** H 78 HIS E 25 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15249 Z= 0.183 Angle : 0.580 8.094 21053 Z= 0.294 Chirality : 0.041 0.154 2418 Planarity : 0.005 0.057 2338 Dihedral : 17.945 173.868 3217 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.68 % Allowed : 14.69 % Favored : 82.63 % 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: -1.37 (0.21), residues: 1571 helix: 0.26 (0.30), residues: 332 sheet: -1.12 (0.28), residues: 352 loop : -1.26 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 380 HIS 0.012 0.001 HIS H 78 PHE 0.017 0.002 PHE K 382 TYR 0.024 0.001 TYR H 97 ARG 0.005 0.000 ARG K 506 *********************** 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 218 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.573 Fit side-chains REVERT: K 310 ARG cc_start: 0.7302 (ptm-80) cc_final: 0.6792 (tpt170) REVERT: G 254 MET cc_start: 0.8645 (mmm) cc_final: 0.8371 (mmp) REVERT: G 260 MET cc_start: 0.7139 (ttt) cc_final: 0.6862 (ttt) REVERT: J 12 ASP cc_start: 0.7771 (p0) cc_final: 0.7413 (t0) REVERT: H 108 GLU cc_start: 0.5436 (mm-30) cc_final: 0.5113 (tp30) REVERT: I 62 ARG cc_start: 0.7351 (mtt-85) cc_final: 0.6847 (mtt90) REVERT: D 93 ASN cc_start: 0.7046 (m110) cc_final: 0.6712 (p0) REVERT: E 121 LYS cc_start: 0.7012 (mmtm) cc_final: 0.6803 (tptt) outliers start: 38 outliers final: 27 residues processed: 203 average time/residue: 0.3175 time to fit residues: 89.4907 Evaluate side-chains 195 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 392 MET 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: 3.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 482 GLN J 31 HIS F 4 GLN ** 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: 0.7413 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 : 0.007 0.074 15249 Z= 0.456 Angle : 0.781 10.842 21053 Z= 0.398 Chirality : 0.049 0.211 2418 Planarity : 0.006 0.059 2338 Dihedral : 18.327 168.536 3217 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.38 % Allowed : 15.68 % Favored : 79.94 % 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: -1.90 (0.21), residues: 1571 helix: -0.41 (0.28), residues: 339 sheet: -1.30 (0.28), residues: 354 loop : -1.59 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 380 HIS 0.006 0.002 HIS G 120 PHE 0.024 0.003 PHE K 382 TYR 0.026 0.003 TYR I 91 ARG 0.009 0.001 ARG H 156 *********************** 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 236 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 1.794 Fit side-chains REVERT: K 224 ASP cc_start: 0.5786 (t0) cc_final: 0.5487 (t0) REVERT: K 310 ARG cc_start: 0.7435 (ptm-80) cc_final: 0.6839 (tpt170) REVERT: G 260 MET cc_start: 0.7329 (ttt) cc_final: 0.7021 (ttt) REVERT: J 12 ASP cc_start: 0.7901 (p0) cc_final: 0.7456 (t0) REVERT: H 77 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7217 (tt) REVERT: H 108 GLU cc_start: 0.5264 (mm-30) cc_final: 0.5035 (tp30) REVERT: I 62 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7175 (mtt-85) REVERT: D 93 ASN cc_start: 0.7222 (m110) cc_final: 0.6875 (p0) REVERT: E 147 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6712 (mt0) REVERT: C 59 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: C 371 MET cc_start: 0.7902 (mtp) cc_final: 0.7567 (mtp) outliers start: 62 outliers final: 45 residues processed: 217 average time/residue: 0.3104 time to fit residues: 95.1748 Evaluate side-chains 216 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 508 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 367 LYS Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15249 Z= 0.190 Angle : 0.607 9.373 21053 Z= 0.306 Chirality : 0.042 0.159 2418 Planarity : 0.005 0.057 2338 Dihedral : 18.009 173.609 3217 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.53 % Allowed : 17.30 % Favored : 79.17 % 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: -1.48 (0.21), residues: 1571 helix: 0.17 (0.29), residues: 335 sheet: -1.15 (0.28), residues: 352 loop : -1.36 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 177 HIS 0.008 0.001 HIS G 103 PHE 0.018 0.002 PHE K 382 TYR 0.015 0.001 TYR H 97 ARG 0.007 0.000 ARG H 156 *********************** 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 229 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 1.513 Fit side-chains REVERT: K 310 ARG cc_start: 0.7424 (ptm-80) cc_final: 0.6821 (tpt170) REVERT: G 254 MET cc_start: 0.8655 (mmm) cc_final: 0.8404 (mmp) REVERT: J 12 ASP cc_start: 0.7759 (p0) cc_final: 0.7475 (t0) REVERT: H 108 GLU cc_start: 0.5230 (mm-30) cc_final: 0.4982 (tp30) REVERT: D 93 ASN cc_start: 0.7246 (m110) cc_final: 0.6903 (p0) REVERT: F 9 GLU cc_start: 0.6506 (pm20) cc_final: 0.6278 (pm20) REVERT: C 59 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8061 (m-10) outliers start: 50 outliers final: 36 residues processed: 209 average time/residue: 0.3262 time to fit residues: 96.4182 Evaluate side-chains 208 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 392 MET 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: 0.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15249 Z= 0.245 Angle : 0.624 9.026 21053 Z= 0.316 Chirality : 0.043 0.170 2418 Planarity : 0.005 0.054 2338 Dihedral : 17.993 171.203 3217 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.95 % Allowed : 17.23 % Favored : 78.81 % 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: -1.45 (0.21), residues: 1571 helix: 0.20 (0.29), residues: 335 sheet: -1.11 (0.28), residues: 352 loop : -1.36 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 380 HIS 0.009 0.001 HIS G 103 PHE 0.020 0.002 PHE K 382 TYR 0.016 0.002 TYR H 97 ARG 0.006 0.000 ARG H 156 *********************** 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 223 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 1.700 Fit side-chains REVERT: K 224 ASP cc_start: 0.5074 (t0) cc_final: 0.4433 (t0) REVERT: K 310 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.6826 (tpt170) REVERT: J 12 ASP cc_start: 0.7852 (p0) cc_final: 0.7502 (t0) REVERT: D 75 GLU cc_start: 0.6610 (pm20) cc_final: 0.6165 (pm20) REVERT: D 93 ASN cc_start: 0.7262 (m110) cc_final: 0.6939 (p0) REVERT: C 59 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: C 215 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6599 (mt) outliers start: 56 outliers final: 47 residues processed: 207 average time/residue: 0.3114 time to fit residues: 90.6745 Evaluate side-chains 213 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 164 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain K residue 508 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 367 LYS Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 460 GLN ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15249 Z= 0.197 Angle : 0.596 8.791 21053 Z= 0.301 Chirality : 0.041 0.155 2418 Planarity : 0.005 0.052 2338 Dihedral : 17.895 172.663 3217 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.81 % Allowed : 17.87 % Favored : 78.32 % 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: -1.29 (0.21), residues: 1571 helix: 0.36 (0.29), residues: 335 sheet: -1.01 (0.29), residues: 352 loop : -1.27 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 354 HIS 0.010 0.001 HIS G 103 PHE 0.018 0.002 PHE K 382 TYR 0.014 0.001 TYR H 97 ARG 0.013 0.000 ARG H 156 *********************** 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 227 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.619 Fit side-chains REVERT: K 310 ARG cc_start: 0.7506 (ptm-80) cc_final: 0.6879 (tpt170) REVERT: J 12 ASP cc_start: 0.7818 (p0) cc_final: 0.7500 (t0) REVERT: I 47 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8017 (mm) REVERT: D 75 GLU cc_start: 0.6601 (pm20) cc_final: 0.6161 (pm20) REVERT: D 93 ASN cc_start: 0.7226 (m110) cc_final: 0.6955 (p0) REVERT: C 59 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: C 215 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6761 (mt) outliers start: 54 outliers final: 45 residues processed: 212 average time/residue: 0.3059 time to fit residues: 91.3455 Evaluate side-chains 213 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 460 GLN Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 367 LYS Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** E 68 GLN E 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15249 Z= 0.167 Angle : 0.569 8.692 21053 Z= 0.286 Chirality : 0.040 0.167 2418 Planarity : 0.005 0.052 2338 Dihedral : 17.788 173.570 3217 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.67 % Allowed : 18.57 % Favored : 77.75 % 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: -1.15 (0.22), residues: 1571 helix: 0.54 (0.30), residues: 335 sheet: -0.97 (0.28), residues: 362 loop : -1.17 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 177 HIS 0.009 0.001 HIS G 103 PHE 0.017 0.001 PHE K 382 TYR 0.015 0.001 TYR I 107 ARG 0.011 0.000 ARG H 156 *********************** 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 227 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.523 Fit side-chains REVERT: K 310 ARG cc_start: 0.7603 (ptm-80) cc_final: 0.6987 (tpt170) REVERT: G 204 MET cc_start: 0.7407 (tpt) cc_final: 0.7037 (tpt) REVERT: J 12 ASP cc_start: 0.7731 (p0) cc_final: 0.7455 (t70) REVERT: I 47 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8006 (mm) REVERT: D 93 ASN cc_start: 0.7235 (m110) cc_final: 0.6948 (p0) REVERT: D 144 PHE cc_start: 0.8151 (m-80) cc_final: 0.7923 (t80) REVERT: F 59 GLN cc_start: 0.5801 (mm110) cc_final: 0.5564 (mm-40) REVERT: E 62 ARG cc_start: 0.5212 (ttm170) cc_final: 0.4502 (ttp-170) REVERT: C 59 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7972 (m-10) outliers start: 52 outliers final: 40 residues processed: 211 average time/residue: 0.3245 time to fit residues: 97.6830 Evaluate side-chains 208 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 367 LYS Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 352 THR 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: 0.0770 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15249 Z= 0.344 Angle : 0.697 10.524 21053 Z= 0.354 Chirality : 0.045 0.211 2418 Planarity : 0.006 0.057 2338 Dihedral : 18.045 169.333 3217 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.74 % Allowed : 18.57 % Favored : 77.68 % 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: -1.49 (0.21), residues: 1571 helix: 0.09 (0.29), residues: 335 sheet: -1.05 (0.28), residues: 350 loop : -1.38 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 380 HIS 0.011 0.001 HIS G 103 PHE 0.022 0.003 PHE K 382 TYR 0.018 0.002 TYR I 91 ARG 0.010 0.001 ARG H 156 ********************** 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 219 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 166 time to evaluate : 1.441 Fit side-chains REVERT: K 224 ASP cc_start: 0.5471 (t0) cc_final: 0.5094 (t0) REVERT: K 310 ARG cc_start: 0.7737 (ptm-80) cc_final: 0.7019 (tpt170) REVERT: J 12 ASP cc_start: 0.7844 (p0) cc_final: 0.7474 (t0) REVERT: I 47 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8004 (mm) REVERT: D 75 GLU cc_start: 0.6715 (pm20) cc_final: 0.6360 (pm20) REVERT: D 93 ASN cc_start: 0.7214 (m110) cc_final: 0.6885 (p0) REVERT: D 144 PHE cc_start: 0.8181 (m-80) cc_final: 0.7903 (t80) REVERT: F 9 GLU cc_start: 0.6432 (pm20) cc_final: 0.6203 (pm20) REVERT: C 59 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: C 215 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6449 (mt) REVERT: C 341 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7686 (pt0) outliers start: 53 outliers final: 43 residues processed: 204 average time/residue: 0.3038 time to fit residues: 87.4308 Evaluate side-chains 209 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 I 32 ASN E 68 GLN E 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.158209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127703 restraints weight = 19428.155| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.56 r_work: 0.3578 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15249 Z= 0.153 Angle : 0.569 8.465 21053 Z= 0.286 Chirality : 0.040 0.160 2418 Planarity : 0.005 0.050 2338 Dihedral : 17.779 174.344 3217 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.90 % Allowed : 19.35 % Favored : 77.75 % 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: -1.12 (0.22), residues: 1571 helix: 0.51 (0.30), residues: 335 sheet: -0.91 (0.29), residues: 353 loop : -1.15 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 177 HIS 0.010 0.001 HIS G 103 PHE 0.017 0.001 PHE K 382 TYR 0.014 0.001 TYR I 107 ARG 0.010 0.000 ARG H 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.27 seconds wall clock time: 61 minutes 17.64 seconds (3677.64 seconds total)