Starting phenix.real_space_refine on Fri Jul 3 23:54:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9a_31813/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_2026/7v9a_31813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9a_31813/07_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-dev-6108/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: {'RNA': 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: 3.71, per 1000 atoms: 0.22 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: 1.28 Conformation dependent library (CDL) restraints added in 730.4 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: 1.73 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: 2.65 Time building geometry restraints manager: 1.81 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=" 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 bond pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.16e-02 7.43e+03 1.65e+00 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 23566 1.36 - 2.73: 714 2.73 - 4.09: 134 4.09 - 5.46: 35 5.46 - 6.82: 9 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=" N VAL C 363 " pdb=" CA VAL C 363 " pdb=" C VAL C 363 " ideal model delta sigma weight residual 113.53 109.70 3.83 9.80e-01 1.04e+00 1.53e+01 ... (remaining 24453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 10024 34.19 - 68.38: 233 68.38 - 102.57: 33 102.57 - 136.76: 1 136.76 - 170.96: 6 Dihedral angle restraints: 10297 sinusoidal: 5311 harmonic: 4986 Sorted by residual: dihedral pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " pdb=" C1' C R 398 " ideal model delta sinusoidal sigma weight residual -35.00 33.12 -68.12 1 8.00e+00 1.56e-02 9.41e+01 dihedral pdb=" C5' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" O3' C R 398 " ideal model delta sinusoidal sigma weight residual 147.00 81.29 65.71 1 8.00e+00 1.56e-02 8.83e+01 dihedral pdb=" O4' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " ideal model delta sinusoidal sigma weight residual 24.00 -34.36 58.36 1 8.00e+00 1.56e-02 7.13e+01 ... (remaining 10294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2519 0.055 - 0.111: 262 0.111 - 0.166: 23 0.166 - 0.222: 0 0.222 - 0.277: 2 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C3' C R 398 " pdb=" C4' C R 398 " pdb=" O3' C R 398 " pdb=" C2' C R 398 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C R 398 " pdb=" C3' C R 398 " pdb=" O2' C R 398 " pdb=" C1' C R 398 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.28e+00 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 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.860 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- 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= 0.126 Angle : 0.579 6.823 24458 Z= 0.353 Chirality : 0.035 0.277 2806 Planarity : 0.004 0.041 2586 Dihedral : 14.821 170.955 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 0.00202 / 0.13 (17553) covalent geometry : angle 0.57914 / 0.35 (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 : 0.626 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: 0.1981 time to fit residues: 85.2618 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 : 0.470 ------------------------------------------------------------------------------- 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 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 = 0.4375 r_free = 0.4375 target = 0.110078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.090232 restraints weight = 66418.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.089736 restraints weight = 62787.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090571 restraints weight = 53032.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.090745 restraints weight = 40336.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.090849 restraints weight = 38066.694| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17553 Z= 0.214 Angle : 0.753 8.730 24458 Z= 0.373 Chirality : 0.044 0.243 2806 Planarity : 0.006 0.051 2586 Dihedral : 12.476 170.775 3642 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.45 % Allowed : 16.63 % Favored : 80.91 % 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: -3.32 (0.18), residues: 1705 helix: -0.65 (0.25), residues: 375 sheet: -2.07 (0.26), residues: 346 loop : -3.02 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 171 TYR 0.020 0.002 TYR J 6 PHE 0.021 0.002 PHE C 59 TRP 0.008 0.002 TRP G 217 HIS 0.009 0.002 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (17553) covalent geometry : angle 0.75268 / 0.37 (24458) hydrogen bonds : bond 0.05525 / 3.76 ( 425) hydrogen bonds : angle 5.50853 / 3.71 ( 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 187 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.7170 (mmm) cc_final: 0.6952 (mmm) REVERT: D 133 MET cc_start: 0.5868 (mmm) cc_final: 0.5547 (mmp) REVERT: E 79 MET cc_start: 0.5992 (mmp) cc_final: 0.5623 (mmp) REVERT: E 128 MET cc_start: 0.4498 (ttp) cc_final: 0.4240 (ttp) REVERT: G 207 TYR cc_start: 0.7398 (t80) cc_final: 0.7110 (t80) REVERT: G 227 ARG cc_start: 0.6856 (ttt180) cc_final: 0.6235 (ttm-80) REVERT: G 371 MET cc_start: 0.5398 (mmm) cc_final: 0.5175 (mtt) outliers start: 37 outliers final: 26 residues processed: 179 average time/residue: 0.1484 time to fit residues: 38.5579 Evaluate side-chains 135 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL 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 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: 5.9990 chunk 172 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 138 optimal weight: 0.0020 chunk 137 optimal weight: 0.1980 chunk 113 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 overall best weight: 2.6192 ------------------------------------------------------------------------------- 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** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 242 GLN G 259 HIS H 106 ASN I 59 GLN J 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.108949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.089469 restraints weight = 67673.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.089095 restraints weight = 66453.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089998 restraints weight = 55359.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.090144 restraints weight = 39983.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090290 restraints weight = 38466.120| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17553 Z= 0.147 Angle : 0.602 8.442 24458 Z= 0.298 Chirality : 0.039 0.205 2806 Planarity : 0.004 0.038 2586 Dihedral : 12.469 169.703 3642 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.98 % Allowed : 19.09 % Favored : 77.93 % 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: -2.90 (0.18), residues: 1705 helix: -0.24 (0.26), residues: 383 sheet: -1.82 (0.26), residues: 340 loop : -2.79 (0.16), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 212 TYR 0.011 0.001 TYR D 149 PHE 0.013 0.001 PHE F 52 TRP 0.008 0.001 TRP G 108 HIS 0.008 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (17553) covalent geometry : angle 0.60227 / 0.30 (24458) hydrogen bonds : bond 0.04125 / 2.74 ( 425) hydrogen bonds : angle 5.07289 / 3.45 ( 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 169 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: D 76 PHE cc_start: 0.5262 (t80) cc_final: 0.4931 (t80) REVERT: D 126 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7487 (p) REVERT: D 134 LYS cc_start: 0.7736 (tppt) cc_final: 0.7490 (tppt) REVERT: F 5 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6641 (p90) REVERT: F 53 LYS cc_start: 0.7118 (mmtm) cc_final: 0.6818 (mmtm) REVERT: G 161 ASN cc_start: 0.7625 (m-40) cc_final: 0.7314 (t0) REVERT: G 227 ARG cc_start: 0.6655 (ttt180) cc_final: 0.5930 (ttm-80) REVERT: G 254 MET cc_start: 0.6051 (mmm) cc_final: 0.5737 (mmm) REVERT: G 371 MET cc_start: 0.5639 (mmm) cc_final: 0.5243 (mtt) REVERT: H 124 TYR cc_start: 0.8341 (m-80) cc_final: 0.8056 (m-80) outliers start: 45 outliers final: 27 residues processed: 156 average time/residue: 0.1240 time to fit residues: 29.9865 Evaluate side-chains 136 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 89 THR Chi-restraints excluded: chain C residue 92 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 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 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 5 TYR 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 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 90 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 0.0030 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.5396 ------------------------------------------------------------------------------- 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 ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 132 HIS H 106 ASN I 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.106959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.087764 restraints weight = 67502.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.087097 restraints weight = 73398.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.087915 restraints weight = 60217.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.088128 restraints weight = 43445.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088227 restraints weight = 41593.688| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17553 Z= 0.146 Angle : 0.616 10.294 24458 Z= 0.305 Chirality : 0.040 0.177 2806 Planarity : 0.004 0.044 2586 Dihedral : 12.647 175.565 3642 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.37 % Allowed : 19.09 % Favored : 76.54 % 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: -2.53 (0.18), residues: 1705 helix: -0.00 (0.27), residues: 383 sheet: -1.40 (0.27), residues: 320 loop : -2.59 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 227 TYR 0.012 0.002 TYR C 273 PHE 0.014 0.001 PHE C 59 TRP 0.010 0.001 TRP G 380 HIS 0.008 0.002 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (17553) covalent geometry : angle 0.61557 / 0.30 (24458) hydrogen bonds : bond 0.03927 / 2.63 ( 425) hydrogen bonds : angle 4.93329 / 3.37 ( 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 183 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 226 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.6907 (mp) REVERT: B 250 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7432 (ttt90) REVERT: B 373 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6144 (tp) REVERT: B 515 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.5447 (mp10) REVERT: F 5 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6416 (p90) REVERT: G 136 ILE cc_start: 0.4697 (OUTLIER) cc_final: 0.4380 (mm) REVERT: G 161 ASN cc_start: 0.7532 (m-40) cc_final: 0.7238 (t0) REVERT: G 227 ARG cc_start: 0.6362 (ttt180) cc_final: 0.6056 (ttm-80) REVERT: G 371 MET cc_start: 0.5275 (mmm) cc_final: 0.5014 (mtt) REVERT: H 124 TYR cc_start: 0.8339 (m-80) cc_final: 0.7961 (m-80) outliers start: 66 outliers final: 44 residues processed: 172 average time/residue: 0.1159 time to fit residues: 30.9560 Evaluate side-chains 149 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 ILE 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 B residue 515 GLN 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 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 311 TYR Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 344 CYS 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 48 TYR 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 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 198 THR Chi-restraints excluded: chain G residue 213 LEU 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 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: 6.9990 chunk 57 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN B 509 HIS B 515 GLN C 264 HIS C 270 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** 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 136 GLN G 276 HIS H 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.103806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.084768 restraints weight = 67762.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084227 restraints weight = 74244.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084877 restraints weight = 62952.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.085148 restraints weight = 45317.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.085217 restraints weight = 43123.969| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17553 Z= 0.194 Angle : 0.679 9.496 24458 Z= 0.340 Chirality : 0.042 0.198 2806 Planarity : 0.005 0.056 2586 Dihedral : 12.980 173.841 3642 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.57 % Allowed : 21.94 % Favored : 73.49 % 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: -2.53 (0.19), residues: 1705 helix: -0.25 (0.26), residues: 385 sheet: -1.32 (0.28), residues: 315 loop : -2.50 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.014 0.002 TYR H 145 PHE 0.016 0.002 PHE C 59 TRP 0.013 0.002 TRP B 257 HIS 0.010 0.002 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (17553) covalent geometry : angle 0.67893 / 0.34 (24458) hydrogen bonds : bond 0.04361 / 2.93 ( 425) hydrogen bonds : angle 5.26394 / 3.54 ( 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 181 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 112 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ARG cc_start: 0.7418 (ttt180) cc_final: 0.7113 (ttt90) REVERT: B 373 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.5976 (tp) REVERT: E 121 LYS cc_start: 0.3894 (OUTLIER) cc_final: 0.3461 (mmmt) REVERT: F 5 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6199 (p90) REVERT: G 371 MET cc_start: 0.5402 (mmm) cc_final: 0.5002 (mtt) REVERT: H 93 ASN cc_start: 0.4567 (OUTLIER) cc_final: 0.4018 (m110) REVERT: H 124 TYR cc_start: 0.8312 (m-80) cc_final: 0.7835 (m-80) outliers start: 69 outliers final: 45 residues processed: 169 average time/residue: 0.1315 time to fit residues: 34.2981 Evaluate side-chains 149 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 217 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 B residue 509 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ARG 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 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 311 TYR 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 344 CYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE 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 143 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR 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 93 ASN 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 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: 2.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 0.0070 chunk 82 optimal weight: 0.3980 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 120 HIS H 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.106417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.087274 restraints weight = 66415.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.086740 restraints weight = 67726.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.087503 restraints weight = 58881.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.087738 restraints weight = 43150.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.087902 restraints weight = 39893.091| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17553 Z= 0.100 Angle : 0.582 10.467 24458 Z= 0.283 Chirality : 0.039 0.179 2806 Planarity : 0.004 0.041 2586 Dihedral : 12.754 176.793 3642 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.84 % Allowed : 22.40 % Favored : 73.76 % 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: 0.15 (0.27), residues: 386 sheet: -0.99 (0.30), residues: 291 loop : -2.34 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.009 0.001 TYR E 139 PHE 0.013 0.001 PHE D 144 TRP 0.011 0.001 TRP B 257 HIS 0.017 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17553) covalent geometry : angle 0.58199 / 0.28 (24458) hydrogen bonds : bond 0.03155 / 2.09 ( 425) hydrogen bonds : angle 4.85784 / 3.29 ( 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 167 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6230 (tp) REVERT: C 243 MET cc_start: 0.6911 (tpp) cc_final: 0.6515 (tpt) REVERT: F 5 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6696 (p90) REVERT: G 227 ARG cc_start: 0.6607 (ttt180) cc_final: 0.5752 (ttm-80) REVERT: G 371 MET cc_start: 0.5421 (mmm) cc_final: 0.5092 (mtt) REVERT: H 93 ASN cc_start: 0.4757 (OUTLIER) cc_final: 0.4096 (m110) REVERT: H 106 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.6928 (t160) REVERT: H 124 TYR cc_start: 0.8184 (m-80) cc_final: 0.7798 (m-80) outliers start: 58 outliers final: 37 residues processed: 159 average time/residue: 0.1358 time to fit residues: 32.8877 Evaluate side-chains 134 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET 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 344 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 31 GLN 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 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 123 THR Chi-restraints excluded: chain G residue 169 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 93 ASN Chi-restraints excluded: chain H residue 106 ASN 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 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 509 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.101846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082174 restraints weight = 67511.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.081852 restraints weight = 64745.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.082375 restraints weight = 64648.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.082779 restraints weight = 45883.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082871 restraints weight = 42441.494| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.6855 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= 0.225 Angle : 0.749 12.375 24458 Z= 0.372 Chirality : 0.044 0.195 2806 Planarity : 0.006 0.042 2586 Dihedral : 13.203 173.849 3642 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.77 % Allowed : 23.53 % Favored : 71.70 % 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: -0.39 (0.26), residues: 385 sheet: -1.28 (0.28), residues: 331 loop : -2.54 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 387 TYR 0.019 0.002 TYR B 244 PHE 0.020 0.002 PHE C 59 TRP 0.017 0.002 TRP B 257 HIS 0.011 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (17553) covalent geometry : angle 0.74869 / 0.37 (24458) hydrogen bonds : bond 0.04820 / 3.22 ( 425) hydrogen bonds : angle 5.41529 / 3.64 ( 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 179 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 107 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6119 (tp) REVERT: C 243 MET cc_start: 0.6952 (tpp) cc_final: 0.6486 (tpt) REVERT: F 5 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6269 (p90) REVERT: G 371 MET cc_start: 0.5474 (mmm) cc_final: 0.5111 (mtt) REVERT: H 93 ASN cc_start: 0.4608 (OUTLIER) cc_final: 0.4071 (m110) REVERT: H 124 TYR cc_start: 0.8429 (m-80) cc_final: 0.8167 (m-80) REVERT: H 155 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6358 (mm-40) outliers start: 72 outliers final: 53 residues processed: 165 average time/residue: 0.1156 time to fit residues: 30.6824 Evaluate side-chains 157 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 100 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 B residue 509 HIS 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 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 311 TYR Chi-restraints excluded: chain C residue 316 MET 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 341 GLU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 31 GLN 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 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 219 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 93 ASN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain I residue 71 VAL 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 17 LEU Chi-restraints excluded: chain J residue 56 MET 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: 7.9990 chunk 104 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 259 HIS H 106 ASN ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.103417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.083938 restraints weight = 67365.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.083566 restraints weight = 66474.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.084218 restraints weight = 61167.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.084609 restraints weight = 44154.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084700 restraints weight = 41456.344| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17553 Z= 0.126 Angle : 0.629 10.161 24458 Z= 0.310 Chirality : 0.040 0.210 2806 Planarity : 0.004 0.054 2586 Dihedral : 13.088 175.567 3642 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.51 % Allowed : 24.78 % Favored : 71.70 % 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: -2.31 (0.19), residues: 1705 helix: -0.13 (0.27), residues: 386 sheet: -1.09 (0.29), residues: 319 loop : -2.37 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.009 0.001 TYR G 86 PHE 0.013 0.001 PHE D 144 TRP 0.010 0.001 TRP B 257 HIS 0.018 0.002 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17553) covalent geometry : angle 0.62902 / 0.31 (24458) hydrogen bonds : bond 0.03607 / 2.40 ( 425) hydrogen bonds : angle 5.08799 / 3.42 ( 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 155 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 MET cc_start: 0.6847 (tpp) cc_final: 0.6450 (tpt) REVERT: C 260 MET cc_start: 0.8190 (tpp) cc_final: 0.7902 (mpp) REVERT: F 5 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6121 (p90) REVERT: G 316 MET cc_start: 0.6950 (mmt) cc_final: 0.6669 (mmt) REVERT: G 371 MET cc_start: 0.5342 (mmm) cc_final: 0.5033 (mtt) REVERT: H 93 ASN cc_start: 0.4677 (OUTLIER) cc_final: 0.4133 (m110) REVERT: H 124 TYR cc_start: 0.8293 (m-80) cc_final: 0.7939 (m-80) outliers start: 53 outliers final: 44 residues processed: 147 average time/residue: 0.1235 time to fit residues: 28.6049 Evaluate side-chains 143 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE 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 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET 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 344 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 91 ASP 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 31 GLN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS 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 169 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 219 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 93 ASN 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 17 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: 0.8980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 259 HIS H 106 ASN ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.083918 restraints weight = 66930.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.083650 restraints weight = 60716.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.084175 restraints weight = 64649.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.084314 restraints weight = 44835.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084480 restraints weight = 41936.254| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17553 Z= 0.130 Angle : 0.629 13.936 24458 Z= 0.307 Chirality : 0.040 0.190 2806 Planarity : 0.004 0.050 2586 Dihedral : 13.070 175.537 3642 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.31 % Allowed : 24.78 % Favored : 71.90 % 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: -2.27 (0.19), residues: 1705 helix: -0.12 (0.27), residues: 386 sheet: -1.02 (0.30), residues: 306 loop : -2.34 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.010 0.001 TYR G 86 PHE 0.010 0.001 PHE C 59 TRP 0.013 0.001 TRP B 257 HIS 0.010 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17553) covalent geometry : angle 0.62908 / 0.31 (24458) hydrogen bonds : bond 0.03629 / 2.38 ( 425) hydrogen bonds : angle 5.06501 / 3.41 ( 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 151 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 243 MET cc_start: 0.7081 (tpp) cc_final: 0.6729 (tpt) REVERT: F 5 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6101 (p90) REVERT: G 371 MET cc_start: 0.5550 (mmm) cc_final: 0.5292 (mtt) REVERT: G 389 LYS cc_start: 0.7020 (mmpt) cc_final: 0.6342 (ttmt) REVERT: H 93 ASN cc_start: 0.4605 (OUTLIER) cc_final: 0.4240 (m110) REVERT: H 124 TYR cc_start: 0.8308 (m-80) cc_final: 0.7943 (m-80) REVERT: H 155 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6651 (mm-40) outliers start: 50 outliers final: 45 residues processed: 143 average time/residue: 0.1092 time to fit residues: 24.7016 Evaluate side-chains 145 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE 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 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 316 MET 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 344 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE 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 31 GLN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS 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 169 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 219 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 71 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ASN 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 12 ASP Chi-restraints excluded: chain J residue 17 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 98 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 ASN ** 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 = 0.4253 r_free = 0.4253 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.083863 restraints weight = 67450.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.083667 restraints weight = 66422.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.084239 restraints weight = 60748.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.084649 restraints weight = 43449.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084765 restraints weight = 40443.576| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17553 Z= 0.134 Angle : 0.636 15.182 24458 Z= 0.312 Chirality : 0.040 0.187 2806 Planarity : 0.004 0.045 2586 Dihedral : 13.112 175.435 3642 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.25 % Allowed : 24.72 % Favored : 72.03 % 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: -2.26 (0.19), residues: 1705 helix: -0.16 (0.26), residues: 386 sheet: -1.01 (0.29), residues: 306 loop : -2.31 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 265 TYR 0.010 0.001 TYR G 86 PHE 0.013 0.001 PHE D 144 TRP 0.012 0.001 TRP B 257 HIS 0.013 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (17553) covalent geometry : angle 0.63640 / 0.31 (24458) hydrogen bonds : bond 0.03649 / 2.40 ( 425) hydrogen bonds : angle 5.06576 / 3.41 ( 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 149 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 MET cc_start: 0.7100 (tpp) cc_final: 0.6762 (tpt) REVERT: F 5 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6095 (p90) REVERT: G 350 MET cc_start: 0.6727 (ptm) cc_final: 0.6441 (ptt) REVERT: G 371 MET cc_start: 0.5509 (mmm) cc_final: 0.5212 (mtt) REVERT: H 93 ASN cc_start: 0.4667 (OUTLIER) cc_final: 0.4322 (m110) REVERT: H 124 TYR cc_start: 0.8317 (m-80) cc_final: 0.7984 (m-80) REVERT: H 155 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6626 (mm-40) outliers start: 49 outliers final: 44 residues processed: 141 average time/residue: 0.1099 time to fit residues: 25.0158 Evaluate side-chains 144 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE 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 109 ILE Chi-restraints excluded: chain C residue 123 THR 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 316 MET 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 344 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE 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 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 202 SER Chi-restraints excluded: chain G residue 219 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 71 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ASN 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 12 ASP Chi-restraints excluded: chain J residue 17 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: 5.9990 chunk 152 optimal weight: 10.0000 chunk 52 optimal weight: 0.0470 chunk 85 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 93 optimal weight: 0.0570 chunk 141 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 ASN ** 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 = 0.4290 r_free = 0.4290 target = 0.105056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085525 restraints weight = 66768.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.085392 restraints weight = 58741.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.086024 restraints weight = 58214.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086126 restraints weight = 41233.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.086311 restraints weight = 38375.697| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17553 Z= 0.098 Angle : 0.587 10.615 24458 Z= 0.285 Chirality : 0.039 0.173 2806 Planarity : 0.004 0.042 2586 Dihedral : 12.932 176.783 3642 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.72 % Allowed : 24.85 % 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: -2.04 (0.19), residues: 1705 helix: 0.05 (0.27), residues: 386 sheet: -0.84 (0.30), residues: 305 loop : -2.19 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 265 TYR 0.010 0.001 TYR E 139 PHE 0.009 0.001 PHE G 59 TRP 0.010 0.001 TRP C 271 HIS 0.010 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (17553) covalent geometry : angle 0.58702 / 0.28 (24458) hydrogen bonds : bond 0.03098 / 1.99 ( 425) hydrogen bonds : angle 4.84521 / 3.27 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.21 seconds wall clock time: 42 minutes 30.23 seconds (2550.23 seconds total)