Starting phenix.real_space_refine on Sat Sep 12 09:07:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7trc_26085/09_2026/7trc_26085.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: 3.17, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 666.3 milliseconds 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: 1.77 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: 2.50 Time building geometry restraints manager: 1.61 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=" C3' C B 379 " pdb=" O3' C B 379 " ideal model delta sigma weight residual 1.415 1.439 -0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 15244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 20202 1.67 - 3.33: 704 3.33 - 5.00: 118 5.00 - 6.66: 24 6.66 - 8.33: 5 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 - 21.30: 8226 21.30 - 42.59: 636 42.59 - 63.89: 171 63.89 - 85.18: 33 85.18 - 106.48: 8 Dihedral angle restraints: 9074 sinusoidal: 4426 harmonic: 4648 Sorted by residual: dihedral pdb=" C4' C B 379 " pdb=" C3' C B 379 " pdb=" C2' C B 379 " pdb=" C1' C B 379 " ideal model delta sinusoidal sigma weight residual 36.35 -42.39 78.73 1 3.10e+00 1.04e-01 8.04e+02 dihedral pdb=" C4' A B 448 " pdb=" C3' A B 448 " pdb=" C2' A B 448 " pdb=" C1' A B 448 " ideal model delta sinusoidal sigma weight residual 36.34 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' A B 378 " pdb=" C3' A B 378 " pdb=" C2' A B 378 " pdb=" C1' A B 378 " ideal model delta sinusoidal sigma weight residual 36.35 -37.45 73.80 1 3.10e+00 1.04e-01 7.20e+02 ... (remaining 9071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2109 0.081 - 0.161: 186 0.161 - 0.242: 82 0.242 - 0.322: 39 0.322 - 0.403: 2 Chirality restraints: 2418 Sorted by residual: chirality pdb=" C2' C B 379 " pdb=" C3' C B 379 " pdb=" O2' C B 379 " pdb=" C1' C B 379 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" P G B 375 " pdb=" OP1 G B 375 " pdb=" OP2 G B 375 " pdb=" O5' G B 375 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C3' C B 379 " pdb=" C4' C B 379 " pdb=" O3' C B 379 " pdb=" C2' C B 379 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.59e+00 ... (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 3.040 nonbonded pdb=" OH TYR G 69 " pdb=" O ILE C 38 " model vdw 2.209 3.040 nonbonded pdb=" O THR K 371 " pdb=" NH1 ARG K 416 " model vdw 2.236 3.120 nonbonded pdb=" O LYS C 57 " pdb=" NH1 ARG C 298 " model vdw 2.272 3.120 nonbonded pdb=" O2' G B 370 " pdb=" N7 A B 372 " model vdw 2.277 3.120 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 48 through 392) selection = (chain 'G' and (resid 48 through 185 or resid 192 through 392)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 68 through 158) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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= 0.149 Angle : 0.737 8.326 21053 Z= 0.379 Chirality : 0.068 0.403 2418 Planarity : 0.005 0.058 2338 Dihedral : 16.362 106.476 6076 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG H 156 TYR 0.014 0.001 TYR I 48 PHE 0.024 0.002 PHE C 59 TRP 0.016 0.001 TRP K 177 HIS 0.006 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15249) covalent geometry : angle 0.73683 / 0.38 (21053) hydrogen bonds : bond 0.23573 / 15.85 ( 438) hydrogen bonds : angle 8.99904 / 6.25 ( 1101) *********************** 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 to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 0.532 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: 0.7179 (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: 0.7042 (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: 0.1539 time to fit residues: 58.4152 Evaluate side-chains 177 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 470 HIS G 77 ASN G 244 GLN H 78 HIS ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN E 32 ASN E 68 GLN C 244 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.156550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126317 restraints weight = 19597.570| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.51 r_work: 0.3552 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1756 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= 0.192 Angle : 0.884 15.514 21053 Z= 0.402 Chirality : 0.081 1.800 2418 Planarity : 0.005 0.061 2338 Dihedral : 14.229 169.846 2851 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.34 % Allowed : 9.11 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.21), residues: 1571 helix: -0.06 (0.29), residues: 339 sheet: -1.36 (0.27), residues: 350 loop : -1.32 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 156 TYR 0.017 0.002 TYR C 281 PHE 0.027 0.002 PHE C 59 TRP 0.018 0.002 TRP G 380 HIS 0.008 0.001 HIS K 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (15249) covalent geometry : angle 0.88444 / 0.40 (21053) hydrogen bonds : bond 0.05584 / 3.42 ( 438) hydrogen bonds : angle 5.96702 / 4.10 ( 1101) *********************** 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 197 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: K 169 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7282 (mp0) REVERT: K 298 ARG cc_start: 0.7646 (ptp-110) cc_final: 0.7253 (mtt180) REVERT: K 307 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.6864 (tpp-160) REVERT: K 310 ARG cc_start: 0.7403 (ptm-80) cc_final: 0.7029 (ptm160) REVERT: G 254 MET cc_start: 0.8862 (mmm) cc_final: 0.8590 (mmp) REVERT: J 12 ASP cc_start: 0.8222 (p0) cc_final: 0.7644 (t0) REVERT: H 108 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5504 (tp30) REVERT: I 42 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7528 (mtp85) REVERT: D 75 GLU cc_start: 0.6912 (mp0) cc_final: 0.6527 (pm20) REVERT: D 133 MET cc_start: 0.5832 (mpp) cc_final: 0.5617 (mpp) REVERT: F 1 MET cc_start: 0.7166 (mmt) cc_final: 0.6748 (mmt) REVERT: E 62 ARG cc_start: 0.5293 (ttm170) cc_final: 0.4586 (ttp-170) REVERT: E 102 ASN cc_start: 0.7645 (t0) cc_final: 0.7354 (t0) outliers start: 19 outliers final: 16 residues processed: 193 average time/residue: 0.1573 time to fit residues: 42.3807 Evaluate side-chains 177 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 G residue 55 LEU 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 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 31 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 HIS J 25 GLN J 31 HIS H 78 HIS D 93 ASN F 4 GLN E 25 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.158906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128857 restraints weight = 19536.364| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.55 r_work: 0.3586 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2115 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= 0.137 Angle : 0.765 13.499 21053 Z= 0.345 Chirality : 0.070 1.592 2418 Planarity : 0.005 0.059 2338 Dihedral : 14.056 174.236 2851 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.77 % Allowed : 12.01 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1571 helix: 0.32 (0.30), residues: 333 sheet: -1.25 (0.27), residues: 357 loop : -1.08 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 122 TYR 0.011 0.001 TYR K 340 PHE 0.026 0.002 PHE E 70 TRP 0.014 0.001 TRP G 380 HIS 0.010 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15249) covalent geometry : angle 0.76543 / 0.34 (21053) hydrogen bonds : bond 0.04591 / 2.69 ( 438) hydrogen bonds : angle 5.35592 / 3.70 ( 1101) *********************** 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 205 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: K 310 ARG cc_start: 0.7397 (ptm-80) cc_final: 0.7050 (ptm160) REVERT: J 12 ASP cc_start: 0.8225 (p0) cc_final: 0.7671 (t0) REVERT: H 108 GLU cc_start: 0.5817 (mm-30) cc_final: 0.5300 (tp30) REVERT: D 75 GLU cc_start: 0.7421 (mp0) cc_final: 0.7140 (pm20) REVERT: D 93 ASN cc_start: 0.7361 (m110) cc_final: 0.6942 (p0) REVERT: D 144 PHE cc_start: 0.8060 (m-80) cc_final: 0.7609 (m-80) REVERT: D 149 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6554 (t80) REVERT: E 62 ARG cc_start: 0.5135 (ttm170) cc_final: 0.4423 (ttp-170) REVERT: E 102 ASN cc_start: 0.7716 (t0) cc_final: 0.7479 (t0) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 0.1537 time to fit residues: 42.3680 Evaluate side-chains 176 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 339 LEU 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 7 LEU Chi-restraints excluded: chain J residue 25 GLN 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 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 202 SER Chi-restraints excluded: chain C residue 236 LEU 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 66 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 482 GLN E 25 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125819 restraints weight = 19686.956| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.43 r_work: 0.3532 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15249 Z= 0.221 Angle : 0.868 14.091 21053 Z= 0.398 Chirality : 0.077 1.499 2418 Planarity : 0.006 0.062 2338 Dihedral : 14.156 171.895 2851 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.32 % Allowed : 13.06 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.21), residues: 1571 helix: 0.04 (0.29), residues: 334 sheet: -1.22 (0.27), residues: 360 loop : -1.29 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 122 TYR 0.020 0.002 TYR K 340 PHE 0.022 0.003 PHE E 70 TRP 0.018 0.002 TRP G 380 HIS 0.007 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (15249) covalent geometry : angle 0.86774 / 0.40 (21053) hydrogen bonds : bond 0.05318 / 3.24 ( 438) hydrogen bonds : angle 5.57578 / 3.84 ( 1101) *********************** 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 213 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.499 Fit side-chains REVERT: K 224 ASP cc_start: 0.5307 (t0) cc_final: 0.4757 (t0) REVERT: K 307 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6866 (tpp-160) REVERT: K 310 ARG cc_start: 0.7509 (ptm-80) cc_final: 0.7246 (ptp-170) REVERT: J 12 ASP cc_start: 0.8273 (p0) cc_final: 0.7711 (t0) REVERT: H 108 GLU cc_start: 0.5794 (mm-30) cc_final: 0.5449 (tp30) REVERT: D 93 ASN cc_start: 0.7275 (m110) cc_final: 0.6931 (p0) REVERT: D 144 PHE cc_start: 0.8106 (m-80) cc_final: 0.7640 (m-80) REVERT: E 62 ARG cc_start: 0.5144 (ttm170) cc_final: 0.4517 (ttp-170) REVERT: E 102 ASN cc_start: 0.7731 (t0) cc_final: 0.7447 (t0) REVERT: C 59 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8131 (m-10) outliers start: 47 outliers final: 34 residues processed: 199 average time/residue: 0.1563 time to fit residues: 43.5466 Evaluate side-chains 196 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 508 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 77 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 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 301 MET 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 392 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 25 GLN E 68 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.159236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129974 restraints weight = 19315.670| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.55 r_work: 0.3594 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2580 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= 0.132 Angle : 0.741 12.204 21053 Z= 0.337 Chirality : 0.066 1.360 2418 Planarity : 0.005 0.061 2338 Dihedral : 13.984 177.007 2851 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.90 % Allowed : 14.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1571 helix: 0.37 (0.29), residues: 336 sheet: -1.09 (0.28), residues: 352 loop : -1.14 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 156 TYR 0.020 0.001 TYR H 97 PHE 0.016 0.002 PHE K 382 TRP 0.015 0.002 TRP G 380 HIS 0.006 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15249) covalent geometry : angle 0.74098 / 0.34 (21053) hydrogen bonds : bond 0.04318 / 2.50 ( 438) hydrogen bonds : angle 5.16277 / 3.57 ( 1101) *********************** 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 209 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.555 Fit side-chains REVERT: K 307 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6986 (tpp-160) REVERT: J 12 ASP cc_start: 0.8247 (p0) cc_final: 0.7579 (t0) REVERT: H 108 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5552 (tp30) REVERT: D 92 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5877 (pm20) REVERT: D 93 ASN cc_start: 0.7257 (m110) cc_final: 0.6800 (p0) REVERT: D 144 PHE cc_start: 0.7917 (m-80) cc_final: 0.7651 (m-80) REVERT: E 62 ARG cc_start: 0.5093 (ttm170) cc_final: 0.4361 (ttp80) REVERT: E 102 ASN cc_start: 0.7788 (t0) cc_final: 0.7505 (t0) REVERT: C 59 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: C 215 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6933 (mt) outliers start: 41 outliers final: 28 residues processed: 195 average time/residue: 0.1520 time to fit residues: 41.9642 Evaluate side-chains 187 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU 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 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 I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 92 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.157736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127306 restraints weight = 19386.408| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.56 r_work: 0.3570 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15249 Z= 0.154 Angle : 0.760 11.642 21053 Z= 0.347 Chirality : 0.067 1.237 2418 Planarity : 0.005 0.056 2338 Dihedral : 13.980 178.405 2851 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.39 % Allowed : 14.76 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1571 helix: 0.38 (0.29), residues: 334 sheet: -1.10 (0.28), residues: 352 loop : -1.14 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 156 TYR 0.016 0.001 TYR H 97 PHE 0.019 0.002 PHE K 382 TRP 0.016 0.002 TRP G 380 HIS 0.007 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (15249) covalent geometry : angle 0.76031 / 0.35 (21053) hydrogen bonds : bond 0.04486 / 2.64 ( 438) hydrogen bonds : angle 5.19130 / 3.58 ( 1101) *********************** 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 215 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.533 Fit side-chains REVERT: K 224 ASP cc_start: 0.5295 (t0) cc_final: 0.4895 (t0) REVERT: K 307 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6940 (tpp-160) REVERT: J 12 ASP cc_start: 0.8177 (p0) cc_final: 0.7587 (t0) REVERT: H 108 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5669 (tp30) REVERT: D 92 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5769 (pm20) REVERT: D 93 ASN cc_start: 0.7397 (m110) cc_final: 0.6899 (p0) REVERT: D 144 PHE cc_start: 0.7937 (m-80) cc_final: 0.7641 (m-80) REVERT: F 61 ARG cc_start: 0.5414 (mmt-90) cc_final: 0.5089 (mmt-90) REVERT: E 62 ARG cc_start: 0.5102 (ttm170) cc_final: 0.4371 (ttp80) REVERT: E 102 ASN cc_start: 0.7805 (t0) cc_final: 0.7517 (t0) REVERT: C 59 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: C 215 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6826 (mt) outliers start: 48 outliers final: 37 residues processed: 202 average time/residue: 0.1405 time to fit residues: 40.3052 Evaluate side-chains 201 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 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 I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 122 ASP 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 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 226 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 335 VAL 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 90 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 136 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.155677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125173 restraints weight = 19493.518| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.55 r_work: 0.3540 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2829 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= 0.197 Angle : 0.820 11.236 21053 Z= 0.378 Chirality : 0.071 1.239 2418 Planarity : 0.005 0.051 2338 Dihedral : 14.085 179.333 2851 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.46 % Allowed : 15.04 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1571 helix: 0.15 (0.29), residues: 336 sheet: -1.20 (0.28), residues: 356 loop : -1.23 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 122 TYR 0.017 0.002 TYR K 340 PHE 0.020 0.002 PHE K 382 TRP 0.018 0.002 TRP G 380 HIS 0.008 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (15249) covalent geometry : angle 0.82030 / 0.38 (21053) hydrogen bonds : bond 0.04912 / 2.94 ( 438) hydrogen bonds : angle 5.35966 / 3.70 ( 1101) *********************** 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 217 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.540 Fit side-chains REVERT: K 224 ASP cc_start: 0.5254 (t0) cc_final: 0.4750 (t0) REVERT: K 307 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.7003 (tpp-160) REVERT: J 12 ASP cc_start: 0.8375 (p0) cc_final: 0.7786 (t0) REVERT: H 108 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5696 (tp30) REVERT: I 41 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.7175 (ttt-90) REVERT: I 62 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6496 (mtt-85) REVERT: D 93 ASN cc_start: 0.7342 (m110) cc_final: 0.6933 (p0) REVERT: D 144 PHE cc_start: 0.7959 (m-80) cc_final: 0.7667 (m-80) REVERT: E 62 ARG cc_start: 0.5122 (ttm170) cc_final: 0.4466 (ttp80) REVERT: E 102 ASN cc_start: 0.7817 (t0) cc_final: 0.7538 (t0) REVERT: C 59 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: C 215 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6708 (mt) outliers start: 49 outliers final: 42 residues processed: 203 average time/residue: 0.1445 time to fit residues: 41.5849 Evaluate side-chains 210 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 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 I residue 132 HIS 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 215 ILE Chi-restraints excluded: chain C residue 226 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 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 83 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122974 restraints weight = 19712.574| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.57 r_work: 0.3509 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15249 Z= 0.241 Angle : 0.879 11.403 21053 Z= 0.407 Chirality : 0.076 1.237 2418 Planarity : 0.006 0.079 2338 Dihedral : 14.222 178.789 2851 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.10 % Allowed : 15.04 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1571 helix: -0.06 (0.29), residues: 330 sheet: -1.30 (0.28), residues: 356 loop : -1.38 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 506 TYR 0.021 0.002 TYR I 91 PHE 0.023 0.003 PHE C 59 TRP 0.021 0.002 TRP G 380 HIS 0.009 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (15249) covalent geometry : angle 0.87889 / 0.41 (21053) hydrogen bonds : bond 0.05417 / 3.27 ( 438) hydrogen bonds : angle 5.58659 / 3.85 ( 1101) *********************** 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 226 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.503 Fit side-chains REVERT: K 224 ASP cc_start: 0.5690 (t0) cc_final: 0.5480 (t0) REVERT: K 307 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7081 (tpp-160) REVERT: J 12 ASP cc_start: 0.8338 (p0) cc_final: 0.7788 (t0) REVERT: H 97 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6089 (t80) REVERT: H 108 GLU cc_start: 0.5951 (mm-30) cc_final: 0.5590 (tp30) REVERT: I 62 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6670 (mtt-85) REVERT: D 75 GLU cc_start: 0.7673 (mp0) cc_final: 0.7451 (pm20) REVERT: D 92 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5835 (pm20) REVERT: D 93 ASN cc_start: 0.7364 (m110) cc_final: 0.6970 (p0) REVERT: E 62 ARG cc_start: 0.5376 (ttm170) cc_final: 0.4815 (ttp-170) REVERT: E 102 ASN cc_start: 0.7813 (t0) cc_final: 0.7535 (t0) REVERT: E 136 GLN cc_start: 0.7419 (tp40) cc_final: 0.7172 (tp40) REVERT: C 59 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: C 215 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6737 (mt) outliers start: 58 outliers final: 45 residues processed: 211 average time/residue: 0.1451 time to fit residues: 43.5624 Evaluate side-chains 216 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 508 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 97 TYR Chi-restraints excluded: chain H residue 106 ASN 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 I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 92 GLU 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 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 226 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 334 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 343 ILE 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 109 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 134 optimal weight: 0.0270 chunk 95 optimal weight: 0.7980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 275 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128370 restraints weight = 19443.233| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.57 r_work: 0.3588 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2966 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= 0.128 Angle : 0.746 11.200 21053 Z= 0.342 Chirality : 0.064 1.258 2418 Planarity : 0.005 0.059 2338 Dihedral : 14.010 177.134 2851 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.68 % Allowed : 17.02 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1571 helix: 0.27 (0.29), residues: 336 sheet: -1.14 (0.28), residues: 352 loop : -1.14 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 156 TYR 0.013 0.001 TYR H 97 PHE 0.017 0.002 PHE K 382 TRP 0.016 0.002 TRP K 177 HIS 0.006 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15249) covalent geometry : angle 0.74564 / 0.34 (21053) hydrogen bonds : bond 0.04318 / 2.46 ( 438) hydrogen bonds : angle 5.12278 / 3.54 ( 1101) *********************** 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 213 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.331 Fit side-chains REVERT: K 224 ASP cc_start: 0.5212 (t0) cc_final: 0.4856 (t0) REVERT: K 307 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6926 (tpp-160) REVERT: G 204 MET cc_start: 0.7585 (tpt) cc_final: 0.7202 (tpt) REVERT: J 12 ASP cc_start: 0.8243 (p0) cc_final: 0.7748 (t0) REVERT: H 108 GLU cc_start: 0.6002 (mm-30) cc_final: 0.5615 (tp30) REVERT: I 41 ARG cc_start: 0.7469 (ttt-90) cc_final: 0.7049 (ttt-90) REVERT: D 92 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5685 (pm20) REVERT: D 93 ASN cc_start: 0.7425 (m110) cc_final: 0.6888 (p0) REVERT: D 144 PHE cc_start: 0.8028 (m-80) cc_final: 0.7623 (t80) REVERT: E 102 ASN cc_start: 0.7863 (t0) cc_final: 0.7597 (t0) REVERT: C 59 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: C 215 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6830 (mt) outliers start: 38 outliers final: 33 residues processed: 200 average time/residue: 0.1498 time to fit residues: 42.4012 Evaluate side-chains 202 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 77 LEU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 122 ASP 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 65 LYS Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 123 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 301 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 48 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.158102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127569 restraints weight = 19471.907| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.58 r_work: 0.3570 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3005 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= 0.152 Angle : 0.773 11.007 21053 Z= 0.356 Chirality : 0.065 1.210 2418 Planarity : 0.005 0.053 2338 Dihedral : 13.996 175.976 2851 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.90 % Allowed : 17.30 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1571 helix: 0.38 (0.29), residues: 330 sheet: -1.05 (0.29), residues: 347 loop : -1.18 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 156 TYR 0.013 0.001 TYR J 41 PHE 0.018 0.002 PHE K 382 TRP 0.015 0.002 TRP G 380 HIS 0.007 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15249) covalent geometry : angle 0.77272 / 0.36 (21053) hydrogen bonds : bond 0.04491 / 2.61 ( 438) hydrogen bonds : angle 5.17051 / 3.56 ( 1101) ********************** 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 203 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.552 Fit side-chains REVERT: K 224 ASP cc_start: 0.5362 (t0) cc_final: 0.4816 (t0) REVERT: K 307 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6976 (tpp-160) REVERT: G 204 MET cc_start: 0.7622 (tpt) cc_final: 0.7234 (tpt) REVERT: J 12 ASP cc_start: 0.8244 (p0) cc_final: 0.7751 (t0) REVERT: H 108 GLU cc_start: 0.6014 (mm-30) cc_final: 0.5638 (tp30) REVERT: D 91 ASP cc_start: 0.6895 (p0) cc_final: 0.6667 (p0) REVERT: D 92 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: D 93 ASN cc_start: 0.7433 (m110) cc_final: 0.6892 (p0) REVERT: D 144 PHE cc_start: 0.8063 (m-80) cc_final: 0.7612 (t80) REVERT: E 102 ASN cc_start: 0.7848 (t0) cc_final: 0.7584 (t0) REVERT: C 59 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8085 (m-10) REVERT: C 215 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6804 (mt) outliers start: 41 outliers final: 37 residues processed: 191 average time/residue: 0.1457 time to fit residues: 39.7303 Evaluate side-chains 200 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 356 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 304 SER 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 77 LEU Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 122 ASP 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 65 LYS 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 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 Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130788 restraints weight = 19162.621| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.55 r_work: 0.3617 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15249 Z= 0.121 Angle : 0.728 13.226 21053 Z= 0.333 Chirality : 0.061 1.204 2418 Planarity : 0.005 0.051 2338 Dihedral : 13.895 178.398 2851 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 18.01 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1571 helix: 0.51 (0.30), residues: 334 sheet: -1.03 (0.29), residues: 353 loop : -1.08 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 156 TYR 0.013 0.001 TYR H 97 PHE 0.016 0.001 PHE K 382 TRP 0.020 0.002 TRP K 177 HIS 0.007 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (15249) covalent geometry : angle 0.72765 / 0.33 (21053) hydrogen bonds : bond 0.04104 / 2.32 ( 438) hydrogen bonds : angle 4.95336 / 3.42 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.99 seconds wall clock time: 79 minutes 38.32 seconds (4778.32 seconds total)