Starting phenix.real_space_refine on Sat Sep 12 16:32:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v9a_31813/09_2026/7v9a_31813.cif" } resolution = 3.94 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 146 5.49 5 S 86 5.16 5 C 10128 2.51 5 N 2999 2.21 5 O 3517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s 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: 16876 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2938 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 25, 'TRANS': 351} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3118 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 16, 'TRANS': 376} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "E" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 526 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "G" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2762 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain: "H" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 123} 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: "R" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3144 Classifications: {'RNAv2': 146} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 70, 'rna3p_pyr': 57} Link IDs: {'rna2p': 19, 'rna3p': 126} Chain breaks: 2 Time building chain proxies: 2.94, per 1000 atoms: 0.17 Number of scatterers: 16876 At special positions: 0 Unit cell: (183.7, 96.8, 132, 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 86 16.00 P 146 15.00 O 3517 8.00 N 2999 7.00 C 10128 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: 1.13 Conformation dependent library (CDL) restraints added in 640.3 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 24.7% alpha, 23.0% beta 16 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.259A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.700A pdb=" N LYS C 57 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 148 removed outlier: 3.785A pdb=" N SER C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.910A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.535A pdb=" N LEU C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 276 removed outlier: 3.525A pdb=" N VAL C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 removed outlier: 3.746A pdb=" N VAL C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.632A pdb=" N LEU C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C 295 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.538A pdb=" N LYS C 413 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 42 through 58 removed outlier: 4.232A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.736A pdb=" N LYS E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 134 through 137 removed outlier: 4.139A pdb=" N GLU E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 138 through 148 removed outlier: 3.624A pdb=" N CYS E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.713A pdb=" N ARG F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 4.096A pdb=" N LYS G 57 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.660A pdb=" N ALA G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 142 through 148 removed outlier: 3.735A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 4.085A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 288 through 292 removed outlier: 3.702A pdb=" N LYS G 291 " --> pdb=" O PRO G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.360A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 385 through 395 Processing helix chain 'H' and resid 148 through 151 removed outlier: 3.809A pdb=" N LEU H 151 " --> pdb=" O PRO H 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 148 through 151' Processing helix chain 'I' and resid 20 through 30 Processing helix chain 'I' and resid 40 through 56 removed outlier: 4.128A pdb=" N LYS I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.788A pdb=" N LYS I 73 " --> pdb=" O LYS I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.502A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 147 removed outlier: 3.999A pdb=" N GLU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 53 removed outlier: 3.911A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 155 through 160 removed outlier: 3.513A pdb=" N ARG B 155 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B 516 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 159 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 514 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 466 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 173 through 177 removed outlier: 3.582A pdb=" N ASN B 187 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 185 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP B 177 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 183 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 218 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 197 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.140A pdb=" N SER B 248 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR B 229 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 246 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TRP B 231 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR B 244 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 254 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 267 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 256 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 293 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 333 removed outlier: 3.521A pdb=" N LEU B 351 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 373 removed outlier: 6.711A pdb=" N GLY B 385 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 373 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE B 383 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 384 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 393 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA B 386 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 391 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 405 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.565A pdb=" N VAL B 429 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 455 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 441 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.581A pdb=" N TYR C 323 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 331 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 368 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 347 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 366 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 364 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 315 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C 244 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG C 158 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU C 246 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 156 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 248 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 154 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 250 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 155 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 214 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 71 through 80 removed outlier: 5.767A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 85 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 111 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.881A pdb=" N VAL D 95 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 152 " --> pdb=" O VAL D 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.517A pdb=" N VAL E 129 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 78 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET E 79 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE E 108 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU E 81 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 13 through 16 removed outlier: 3.611A pdb=" N VAL F 14 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 5 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS F 28 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.559A pdb=" N TYR G 323 " --> pdb=" O ASN G 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 119 through 120 removed outlier: 3.733A pdb=" N GLY G 119 " --> pdb=" O CYS G 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 132 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 94 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL G 261 " --> pdb=" O PHE G 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN G 93 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 178 through 182 removed outlier: 3.828A pdb=" N ARG G 197 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 201 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU G 152 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 249 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 245 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG G 158 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET G 243 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET G 254 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 298 through 300 removed outlier: 5.841A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN G 331 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS G 344 " --> pdb=" O VAL G 335 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 368 " --> pdb=" O MET G 345 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE G 347 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE G 366 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 80 removed outlier: 5.278A pdb=" N PHE H 76 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS H 87 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY H 111 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 61 removed outlier: 3.891A pdb=" N ILE I 78 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 13 through 16 removed outlier: 3.629A pdb=" N VAL J 14 " --> pdb=" O TYR J 6 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 4 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS J 28 " --> pdb=" O TYR J 5 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4860 1.34 - 1.46: 3643 1.46 - 1.57: 8636 1.57 - 1.69: 289 1.69 - 1.81: 125 Bond restraints: 17553 Sorted by residual: bond pdb=" C LEU H 158 " pdb=" N PRO H 159 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.11e-02 8.12e+03 3.33e+00 bond pdb=" CA TYR E 91 " pdb=" CB TYR E 91 " ideal model delta sigma weight residual 1.528 1.568 -0.039 2.61e-02 1.47e+03 2.27e+00 bond pdb=" C GLY B 444 " pdb=" N PRO B 445 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.79e+00 bond pdb=" C3' G R 393 " pdb=" O3' G R 393 " ideal model delta sigma weight residual 1.415 1.442 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" N LEU G 54 " pdb=" CA LEU G 54 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 23157 1.36 - 2.73: 987 2.73 - 4.09: 231 4.09 - 5.46: 72 5.46 - 6.82: 11 Bond angle restraints: 24458 Sorted by residual: angle pdb=" CA ASP D 91 " pdb=" C ASP D 91 " pdb=" N GLU D 92 " ideal model delta sigma weight residual 118.81 113.40 5.41 1.15e+00 7.56e-01 2.21e+01 angle pdb=" N VAL C 239 " pdb=" CA VAL C 239 " pdb=" C VAL C 239 " ideal model delta sigma weight residual 113.71 109.66 4.05 9.50e-01 1.11e+00 1.82e+01 angle pdb=" N VAL G 239 " pdb=" CA VAL G 239 " pdb=" C VAL G 239 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" C PRO C 53 " pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 120.79 126.37 -5.58 1.39e+00 5.18e-01 1.61e+01 angle pdb=" C3' G R 393 " pdb=" O3' G R 393 " pdb=" P C R 394 " ideal model delta sigma weight residual 119.70 124.42 -4.72 1.20e+00 6.94e-01 1.55e+01 ... (remaining 24453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 9859 34.19 - 68.38: 390 68.38 - 102.57: 42 102.57 - 136.76: 0 136.76 - 170.96: 6 Dihedral angle restraints: 10297 sinusoidal: 5311 harmonic: 4986 Sorted by residual: dihedral pdb=" C4' A R 448 " pdb=" C3' A R 448 " pdb=" C2' A R 448 " pdb=" C1' A R 448 " ideal model delta sinusoidal sigma weight residual 36.34 -37.64 73.99 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' C R 379 " pdb=" C3' C R 379 " pdb=" C2' C R 379 " pdb=" C1' C R 379 " ideal model delta sinusoidal sigma weight residual 36.34 -37.03 73.37 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" C4' A R 378 " pdb=" C3' A R 378 " pdb=" C2' A R 378 " pdb=" C1' A R 378 " ideal model delta sinusoidal sigma weight residual 36.34 -36.30 72.65 1 3.10e+00 1.04e-01 7.01e+02 ... (remaining 10294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2475 0.078 - 0.156: 150 0.156 - 0.234: 61 0.234 - 0.312: 118 0.312 - 0.391: 2 Chirality restraints: 2806 Sorted by residual: chirality pdb=" P C R 394 " pdb=" OP1 C R 394 " pdb=" OP2 C R 394 " pdb=" O5' C R 394 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" P C R 415 " pdb=" OP1 C R 415 " pdb=" OP2 C R 415 " pdb=" O5' C R 415 " 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=" P G R 399 " pdb=" OP1 G R 399 " pdb=" OP2 G R 399 " pdb=" O5' G R 399 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2803 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 158 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 159 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 52 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 53 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 500 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 501 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.021 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3643 2.79 - 3.32: 13897 3.32 - 3.84: 26781 3.84 - 4.37: 30435 4.37 - 4.90: 51103 Nonbonded interactions: 125859 Sorted by model distance: nonbonded pdb=" O LYS G 291 " pdb=" OG1 THR G 294 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP B 422 " pdb=" OG1 THR B 424 " model vdw 2.285 3.040 nonbonded pdb=" O GLY C 383 " pdb=" OG SER C 387 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP B 180 " pdb=" OG SER B 182 " model vdw 2.292 3.040 nonbonded pdb=" O ASP G 85 " pdb=" OG1 THR G 89 " model vdw 2.295 3.040 ... (remaining 125854 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 47 through 395) selection = chain 'G' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 22 through 150) } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 1 through 62) } 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 group one per residue 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: 5.860 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 14.880 Find NCS groups from input model: 0.190 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 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 : 0.002 0.039 17553 Z= 0.136 Angle : 0.700 6.823 24458 Z= 0.383 Chirality : 0.071 0.391 2806 Planarity : 0.004 0.041 2586 Dihedral : 16.775 170.955 7097 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -4.05 (0.16), residues: 1705 helix: -1.49 (0.23), residues: 379 sheet: -2.27 (0.27), residues: 301 loop : -3.49 (0.14), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 141 TYR 0.008 0.001 TYR E 91 PHE 0.009 0.001 PHE B 419 TRP 0.010 0.001 TRP C 52 HIS 0.002 0.000 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (17553) covalent geometry : angle 0.70049 / 0.38 (24458) hydrogen bonds : bond 0.23041 / 14.38 ( 425) hydrogen bonds : angle 8.42022 / 5.57 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8331 (mptt) cc_final: 0.8029 (mmtm) REVERT: D 146 ILE cc_start: 0.7064 (tt) cc_final: 0.6299 (tt) REVERT: G 133 ILE cc_start: 0.5893 (mm) cc_final: 0.5675 (mm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1811 time to fit residues: 78.2139 Evaluate side-chains 141 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS C 147 GLN C 160 HIS C 244 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 63 ASN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN G 307 ASN G 331 GLN H 64 GLN I 31 GLN I 68 GLN J 59 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.111318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.092010 restraints weight = 66687.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.091537 restraints weight = 70501.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.092348 restraints weight = 59690.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.092592 restraints weight = 43195.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.092730 restraints weight = 40181.870| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17553 Z= 0.233 Angle : 0.969 19.904 24458 Z= 0.425 Chirality : 0.073 0.885 2806 Planarity : 0.006 0.072 2586 Dihedral : 14.805 167.181 3642 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.78 % Allowed : 15.18 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -3.25 (0.18), residues: 1705 helix: -0.51 (0.26), residues: 374 sheet: -1.94 (0.26), residues: 337 loop : -3.05 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 347 TYR 0.017 0.002 TYR J 6 PHE 0.020 0.002 PHE C 181 TRP 0.008 0.001 TRP G 217 HIS 0.006 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (17553) covalent geometry : angle 0.96910 / 0.42 (24458) hydrogen bonds : bond 0.05155 / 3.45 ( 425) hydrogen bonds : angle 5.46244 / 3.68 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.5758 (mmm) cc_final: 0.5403 (mmt) REVERT: E 79 MET cc_start: 0.5839 (mmp) cc_final: 0.5554 (mmp) REVERT: E 128 MET cc_start: 0.4769 (ttp) cc_final: 0.4379 (ttp) REVERT: G 207 TYR cc_start: 0.7367 (t80) cc_final: 0.7102 (t80) REVERT: G 227 ARG cc_start: 0.6975 (ttt180) cc_final: 0.6557 (ttt90) REVERT: G 345 MET cc_start: 0.5579 (ptp) cc_final: 0.5285 (mtp) REVERT: G 371 MET cc_start: 0.5422 (mmm) cc_final: 0.5178 (mtt) outliers start: 42 outliers final: 30 residues processed: 177 average time/residue: 0.1437 time to fit residues: 37.2616 Evaluate side-chains 142 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS J 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.089812 restraints weight = 67393.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.089486 restraints weight = 70345.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.090181 restraints weight = 58012.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090372 restraints weight = 43514.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090475 restraints weight = 40780.581| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17553 Z= 0.165 Angle : 0.781 17.025 24458 Z= 0.348 Chirality : 0.059 0.580 2806 Planarity : 0.004 0.038 2586 Dihedral : 14.769 167.714 3642 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.11 % Allowed : 18.56 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.88 (0.18), residues: 1705 helix: -0.25 (0.26), residues: 383 sheet: -1.82 (0.26), residues: 333 loop : -2.76 (0.16), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 51 TYR 0.011 0.001 TYR E 139 PHE 0.013 0.001 PHE C 59 TRP 0.008 0.001 TRP G 108 HIS 0.009 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17553) covalent geometry : angle 0.78136 / 0.35 (24458) hydrogen bonds : bond 0.03899 / 2.52 ( 425) hydrogen bonds : angle 5.11031 / 3.47 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 PHE cc_start: 0.5261 (t80) cc_final: 0.4932 (t80) REVERT: D 126 SER cc_start: 0.7618 (OUTLIER) cc_final: 0.7355 (p) REVERT: D 133 MET cc_start: 0.6056 (mmm) cc_final: 0.5833 (mmp) REVERT: D 134 LYS cc_start: 0.7623 (tppt) cc_final: 0.7412 (tppt) REVERT: G 161 ASN cc_start: 0.7608 (m-40) cc_final: 0.7327 (t0) REVERT: G 227 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.5715 (ttm170) REVERT: G 254 MET cc_start: 0.5998 (mmm) cc_final: 0.5680 (mmm) REVERT: G 345 MET cc_start: 0.5866 (ptp) cc_final: 0.5539 (mtp) REVERT: G 371 MET cc_start: 0.5638 (mmm) cc_final: 0.5222 (mtt) REVERT: H 124 TYR cc_start: 0.8291 (m-80) cc_final: 0.8019 (m-80) outliers start: 47 outliers final: 28 residues processed: 162 average time/residue: 0.1266 time to fit residues: 31.9742 Evaluate side-chains 139 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 0.0470 chunk 124 optimal weight: 0.4980 chunk 172 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN B 460 GLN B 515 GLN D 59 ASN D 99 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.109935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.090173 restraints weight = 67505.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090065 restraints weight = 62687.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.090707 restraints weight = 52840.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.091020 restraints weight = 39714.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.091085 restraints weight = 37032.489| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17553 Z= 0.114 Angle : 0.706 14.071 24458 Z= 0.310 Chirality : 0.055 0.452 2806 Planarity : 0.004 0.042 2586 Dihedral : 14.425 170.789 3642 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.72 % Allowed : 20.21 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.49 (0.18), residues: 1705 helix: 0.12 (0.27), residues: 384 sheet: -1.37 (0.27), residues: 322 loop : -2.61 (0.17), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 227 TYR 0.010 0.001 TYR E 139 PHE 0.010 0.001 PHE G 59 TRP 0.006 0.001 TRP B 517 HIS 0.007 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17553) covalent geometry : angle 0.70638 / 0.31 (24458) hydrogen bonds : bond 0.03094 / 2.02 ( 425) hydrogen bonds : angle 4.79386 / 3.28 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: G 254 MET cc_start: 0.6251 (mmm) cc_final: 0.6041 (mmm) REVERT: G 345 MET cc_start: 0.5974 (ptp) cc_final: 0.5607 (mtp) REVERT: G 371 MET cc_start: 0.5624 (mmm) cc_final: 0.5312 (mtt) REVERT: H 124 TYR cc_start: 0.8228 (m-80) cc_final: 0.7922 (m-80) outliers start: 41 outliers final: 28 residues processed: 149 average time/residue: 0.1453 time to fit residues: 32.8357 Evaluate side-chains 130 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 85 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS I 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.087094 restraints weight = 68454.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.086485 restraints weight = 81298.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.086997 restraints weight = 77566.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.087452 restraints weight = 55748.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.087541 restraints weight = 49759.118| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17553 Z= 0.213 Angle : 0.857 11.536 24458 Z= 0.389 Chirality : 0.059 0.440 2806 Planarity : 0.005 0.049 2586 Dihedral : 14.689 170.060 3642 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.57 % Allowed : 20.74 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.59 (0.18), residues: 1705 helix: -0.16 (0.26), residues: 382 sheet: -1.38 (0.28), residues: 319 loop : -2.59 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 265 TYR 0.015 0.002 TYR B 352 PHE 0.018 0.002 PHE C 59 TRP 0.015 0.002 TRP G 380 HIS 0.010 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (17553) covalent geometry : angle 0.85654 / 0.39 (24458) hydrogen bonds : bond 0.04612 / 3.08 ( 425) hydrogen bonds : angle 5.27256 / 3.56 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 115 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.4921 (tpt) cc_final: 0.4609 (tpt) REVERT: B 250 ARG cc_start: 0.7711 (ttt180) cc_final: 0.7416 (ttt90) REVERT: B 373 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6007 (tp) REVERT: E 79 MET cc_start: 0.6365 (mmt) cc_final: 0.6163 (mmt) REVERT: E 121 LYS cc_start: 0.4040 (OUTLIER) cc_final: 0.3648 (mmmt) REVERT: F 5 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6273 (p90) REVERT: G 136 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4718 (mm) REVERT: G 227 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5669 (ttm170) REVERT: G 345 MET cc_start: 0.5945 (ptp) cc_final: 0.5492 (mtp) REVERT: G 371 MET cc_start: 0.5215 (mmm) cc_final: 0.4979 (mtt) REVERT: H 124 TYR cc_start: 0.8392 (m-80) cc_final: 0.7910 (m-80) outliers start: 69 outliers final: 40 residues processed: 171 average time/residue: 0.1261 time to fit residues: 33.4837 Evaluate side-chains 143 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 0.0170 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 overall best weight: 0.9236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.107474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.088689 restraints weight = 66506.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.088426 restraints weight = 68252.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.088951 restraints weight = 61276.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.089295 restraints weight = 43871.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.089383 restraints weight = 41169.378| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17553 Z= 0.111 Angle : 0.713 9.206 24458 Z= 0.315 Chirality : 0.054 0.354 2806 Planarity : 0.004 0.043 2586 Dihedral : 14.504 172.701 3642 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.98 % Allowed : 22.27 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.25 (0.19), residues: 1705 helix: 0.18 (0.27), residues: 387 sheet: -1.10 (0.29), residues: 308 loop : -2.43 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.009 0.001 TYR E 139 PHE 0.012 0.001 PHE D 144 TRP 0.010 0.001 TRP B 257 HIS 0.007 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17553) covalent geometry : angle 0.71288 / 0.31 (24458) hydrogen bonds : bond 0.03172 / 2.09 ( 425) hydrogen bonds : angle 4.83417 / 3.28 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5031 (tpt) cc_final: 0.4639 (tpt) REVERT: C 54 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7130 (pt) REVERT: C 243 MET cc_start: 0.6699 (tpp) cc_final: 0.6456 (tpt) REVERT: E 79 MET cc_start: 0.6326 (mmt) cc_final: 0.6029 (mmp) REVERT: G 136 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.4237 (mm) REVERT: G 316 MET cc_start: 0.6450 (mmt) cc_final: 0.6098 (mmt) REVERT: G 345 MET cc_start: 0.6209 (ptp) cc_final: 0.5869 (mtp) REVERT: G 350 MET cc_start: 0.7212 (ptm) cc_final: 0.6961 (ptp) REVERT: G 371 MET cc_start: 0.5356 (mmm) cc_final: 0.4956 (mtt) REVERT: H 124 TYR cc_start: 0.8086 (m-80) cc_final: 0.7732 (m-80) outliers start: 45 outliers final: 30 residues processed: 143 average time/residue: 0.1393 time to fit residues: 30.2286 Evaluate side-chains 125 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 GLN ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS G 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.101718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.082526 restraints weight = 67889.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.082272 restraints weight = 71090.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.082778 restraints weight = 66856.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.083238 restraints weight = 46775.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.083360 restraints weight = 43724.404| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17553 Z= 0.257 Angle : 0.934 11.609 24458 Z= 0.424 Chirality : 0.062 0.450 2806 Planarity : 0.006 0.055 2586 Dihedral : 14.938 173.835 3642 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.24 % Allowed : 22.66 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.63 (0.19), residues: 1705 helix: -0.49 (0.25), residues: 382 sheet: -1.24 (0.29), residues: 315 loop : -2.54 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 347 TYR 0.018 0.002 TYR G 86 PHE 0.022 0.002 PHE C 59 TRP 0.021 0.002 TRP G 380 HIS 0.013 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (17553) covalent geometry : angle 0.93354 / 0.42 (24458) hydrogen bonds : bond 0.05235 / 3.55 ( 425) hydrogen bonds : angle 5.53671 / 3.73 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 108 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5133 (tpt) cc_final: 0.4496 (tpt) REVERT: B 373 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6142 (tp) REVERT: C 260 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7821 (mmt) REVERT: C 332 GLU cc_start: 0.6740 (tp30) cc_final: 0.6420 (pm20) REVERT: E 79 MET cc_start: 0.6644 (mmt) cc_final: 0.6407 (mmt) REVERT: F 5 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6282 (p90) REVERT: G 227 ARG cc_start: 0.6497 (OUTLIER) cc_final: 0.5769 (ttm170) REVERT: G 301 MET cc_start: 0.8085 (mmm) cc_final: 0.7836 (mmm) REVERT: G 371 MET cc_start: 0.5450 (mmm) cc_final: 0.5037 (mtt) REVERT: H 124 TYR cc_start: 0.8387 (m-80) cc_final: 0.8106 (m-80) outliers start: 64 outliers final: 44 residues processed: 162 average time/residue: 0.1211 time to fit residues: 31.6286 Evaluate side-chains 147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 158 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 50 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 GLN ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS G 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.104514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.085392 restraints weight = 67987.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.085226 restraints weight = 68197.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.085793 restraints weight = 61954.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.086236 restraints weight = 43010.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.086448 restraints weight = 40146.548| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17553 Z= 0.128 Angle : 0.756 9.298 24458 Z= 0.336 Chirality : 0.056 0.359 2806 Planarity : 0.005 0.055 2586 Dihedral : 14.674 176.699 3642 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.11 % Allowed : 24.45 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.33 (0.19), residues: 1705 helix: -0.09 (0.27), residues: 385 sheet: -1.11 (0.28), residues: 331 loop : -2.41 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 227 TYR 0.015 0.001 TYR F 5 PHE 0.011 0.001 PHE D 144 TRP 0.010 0.001 TRP C 271 HIS 0.008 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17553) covalent geometry : angle 0.75561 / 0.34 (24458) hydrogen bonds : bond 0.03559 / 2.37 ( 425) hydrogen bonds : angle 5.06064 / 3.43 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5037 (tpt) cc_final: 0.4451 (tpt) REVERT: C 260 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: C 382 LEU cc_start: 0.6959 (tp) cc_final: 0.6726 (tp) REVERT: E 79 MET cc_start: 0.6675 (mmt) cc_final: 0.6389 (mmp) REVERT: E 99 GLU cc_start: 0.6945 (pp20) cc_final: 0.6586 (mm-30) REVERT: E 128 MET cc_start: 0.4671 (ttt) cc_final: 0.4331 (ttp) REVERT: G 227 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5775 (ttm170) REVERT: G 371 MET cc_start: 0.5471 (mmm) cc_final: 0.5172 (mtt) REVERT: H 124 TYR cc_start: 0.8210 (m-80) cc_final: 0.7719 (m-80) REVERT: J 23 MET cc_start: 0.5707 (tpp) cc_final: 0.5445 (tpp) outliers start: 47 outliers final: 36 residues processed: 142 average time/residue: 0.1278 time to fit residues: 28.8894 Evaluate side-chains 132 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS C 401 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS G 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082754 restraints weight = 68441.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082616 restraints weight = 73291.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.083127 restraints weight = 66329.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083502 restraints weight = 47011.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.083621 restraints weight = 44259.069| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17553 Z= 0.229 Angle : 0.891 11.188 24458 Z= 0.403 Chirality : 0.060 0.432 2806 Planarity : 0.006 0.053 2586 Dihedral : 14.899 174.826 3642 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.31 % Allowed : 24.25 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.59 (0.19), residues: 1705 helix: -0.53 (0.25), residues: 387 sheet: -1.27 (0.29), residues: 317 loop : -2.47 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 61 TYR 0.018 0.002 TYR G 86 PHE 0.020 0.002 PHE C 59 TRP 0.022 0.002 TRP G 380 HIS 0.010 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (17553) covalent geometry : angle 0.89081 / 0.40 (24458) hydrogen bonds : bond 0.04875 / 3.27 ( 425) hydrogen bonds : angle 5.47026 / 3.69 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5141 (tpt) cc_final: 0.4525 (tpt) REVERT: C 301 MET cc_start: 0.8464 (tmm) cc_final: 0.7734 (tmm) REVERT: C 332 GLU cc_start: 0.6711 (tp30) cc_final: 0.6317 (pm20) REVERT: D 144 PHE cc_start: 0.7452 (m-80) cc_final: 0.6990 (m-80) REVERT: E 128 MET cc_start: 0.4823 (ttt) cc_final: 0.4498 (ttt) REVERT: F 5 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5998 (p90) REVERT: G 227 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5705 (ttm170) REVERT: G 350 MET cc_start: 0.7142 (ptm) cc_final: 0.6771 (ptm) REVERT: G 371 MET cc_start: 0.5341 (mmm) cc_final: 0.4962 (mtt) REVERT: H 124 TYR cc_start: 0.8371 (m-80) cc_final: 0.8153 (m-80) REVERT: J 23 MET cc_start: 0.5839 (tpp) cc_final: 0.5573 (tpp) outliers start: 50 outliers final: 43 residues processed: 142 average time/residue: 0.1265 time to fit residues: 28.5817 Evaluate side-chains 144 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.0770 chunk 37 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** I 132 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 = 0.4265 r_free = 0.4265 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085309 restraints weight = 68218.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.085585 restraints weight = 67364.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.085888 restraints weight = 65889.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.086328 restraints weight = 43287.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.086556 restraints weight = 39082.150| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17553 Z= 0.128 Angle : 0.766 10.393 24458 Z= 0.343 Chirality : 0.056 0.348 2806 Planarity : 0.005 0.049 2586 Dihedral : 14.659 175.748 3642 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.85 % Allowed : 24.98 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.34 (0.19), residues: 1705 helix: -0.13 (0.27), residues: 385 sheet: -1.08 (0.29), residues: 321 loop : -2.40 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 65 TYR 0.013 0.001 TYR F 5 PHE 0.028 0.001 PHE H 123 TRP 0.011 0.001 TRP C 217 HIS 0.010 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17553) covalent geometry : angle 0.76562 / 0.34 (24458) hydrogen bonds : bond 0.03554 / 2.31 ( 425) hydrogen bonds : angle 5.07887 / 3.44 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.4974 (tpt) cc_final: 0.4392 (tpt) REVERT: C 260 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: D 144 PHE cc_start: 0.7500 (m-80) cc_final: 0.7045 (m-80) REVERT: E 106 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8594 (p) REVERT: F 1 MET cc_start: 0.6395 (ppp) cc_final: 0.5578 (ptp) REVERT: F 5 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5847 (p90) REVERT: G 227 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5920 (ttm170) REVERT: G 371 MET cc_start: 0.5781 (mmm) cc_final: 0.5537 (mtt) REVERT: G 389 LYS cc_start: 0.7134 (mmpt) cc_final: 0.6726 (ptpt) REVERT: H 124 TYR cc_start: 0.8392 (m-80) cc_final: 0.7940 (m-80) outliers start: 43 outliers final: 36 residues processed: 139 average time/residue: 0.1282 time to fit residues: 28.1408 Evaluate side-chains 139 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 33 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 52 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** I 132 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 = 0.4269 r_free = 0.4269 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.085540 restraints weight = 68067.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.084665 restraints weight = 79310.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.085581 restraints weight = 64355.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.085841 restraints weight = 45228.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.085961 restraints weight = 43665.079| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17553 Z= 0.122 Angle : 0.747 9.754 24458 Z= 0.333 Chirality : 0.055 0.351 2806 Planarity : 0.005 0.043 2586 Dihedral : 14.524 174.674 3642 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.72 % Allowed : 24.98 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.18 (0.19), residues: 1705 helix: 0.00 (0.27), residues: 385 sheet: -0.96 (0.29), residues: 317 loop : -2.31 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 65 TYR 0.013 0.001 TYR F 5 PHE 0.024 0.001 PHE H 123 TRP 0.009 0.001 TRP B 395 HIS 0.006 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17553) covalent geometry : angle 0.74705 / 0.33 (24458) hydrogen bonds : bond 0.03460 / 2.22 ( 425) hydrogen bonds : angle 4.98779 / 3.38 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.01 seconds wall clock time: 42 minutes 49.41 seconds (2569.41 seconds total)