Starting phenix.real_space_refine on Wed Mar 4 22:45:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9a_31813/03_2026/7v9a_31813.map" } 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-5986/lib/python3.9/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: 3.88, per 1000 atoms: 0.23 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: 1.41 Conformation dependent library (CDL) restraints added in 541.1 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: 1.58 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: 3.00 Time building geometry restraints manager: 1.84 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: 10279 34.19 - 68.38: 550 68.38 - 102.57: 77 102.57 - 136.76: 1 136.76 - 170.96: 6 Dihedral angle restraints: 10913 sinusoidal: 5927 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 10910 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: 6.320 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 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 : 18.983 170.955 7713 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 covalent geometry : bond 0.00202 (17553) covalent geometry : angle 0.57914 (24458) hydrogen bonds : bond 0.23041 ( 425) hydrogen bonds : angle 8.42022 ( 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 : 0.571 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: 0.1915 time to fit residues: 81.6450 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 : 0.559 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 252 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.109399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.089869 restraints weight = 67074.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.089423 restraints weight = 66754.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090204 restraints weight = 59980.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.090302 restraints weight = 43748.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090467 restraints weight = 40500.694| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17553 Z= 0.217 Angle : 0.762 8.748 24458 Z= 0.379 Chirality : 0.045 0.327 2806 Planarity : 0.006 0.067 2586 Dihedral : 20.322 171.900 4258 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.85 % Allowed : 16.63 % Favored : 80.52 % 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: -3.35 (0.17), residues: 1705 helix: -0.72 (0.25), residues: 375 sheet: -2.13 (0.25), residues: 352 loop : -3.00 (0.16), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 171 TYR 0.020 0.002 TYR J 6 PHE 0.021 0.002 PHE C 59 TRP 0.010 0.002 TRP G 217 HIS 0.008 0.002 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00486 (17553) covalent geometry : angle 0.76186 (24458) hydrogen bonds : bond 0.05842 ( 425) hydrogen bonds : angle 5.54880 ( 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: 43 poor density : 144 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.5930 (mmm) cc_final: 0.5581 (mmp) REVERT: E 79 MET cc_start: 0.6051 (mmp) cc_final: 0.5529 (mmp) REVERT: E 128 MET cc_start: 0.4543 (ttp) cc_final: 0.4125 (ttp) REVERT: G 207 TYR cc_start: 0.7413 (t80) cc_final: 0.7098 (t80) REVERT: G 227 ARG cc_start: 0.6878 (ttt180) cc_final: 0.5918 (ttm-80) REVERT: G 371 MET cc_start: 0.5583 (mmm) cc_final: 0.5285 (mtt) outliers start: 43 outliers final: 30 residues processed: 177 average time/residue: 0.1464 time to fit residues: 37.7754 Evaluate side-chains 140 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL 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 94 LEU 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 68 GLN 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 G residue 333 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: 0.9990 chunk 172 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 93 ASN D 59 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 242 GLN G 259 HIS H 106 ASN I 68 GLN J 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.110368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.090737 restraints weight = 67645.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.090503 restraints weight = 65642.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.091320 restraints weight = 52651.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.091456 restraints weight = 39672.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.091548 restraints weight = 38207.108| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17553 Z= 0.111 Angle : 0.574 9.144 24458 Z= 0.281 Chirality : 0.038 0.174 2806 Planarity : 0.004 0.035 2586 Dihedral : 20.191 171.599 4258 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.72 % Allowed : 18.69 % Favored : 78.60 % 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: -2.86 (0.18), residues: 1705 helix: -0.19 (0.26), residues: 382 sheet: -1.89 (0.26), residues: 344 loop : -2.72 (0.16), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.012 0.001 TYR D 149 PHE 0.009 0.001 PHE H 138 TRP 0.015 0.001 TRP G 52 HIS 0.008 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00246 (17553) covalent geometry : angle 0.57402 (24458) hydrogen bonds : bond 0.03654 ( 425) hydrogen bonds : angle 4.97031 ( 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 171 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 293 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7343 (pt) REVERT: D 126 SER cc_start: 0.7951 (t) cc_final: 0.7687 (p) REVERT: D 134 LYS cc_start: 0.7731 (tppt) cc_final: 0.7426 (tppt) REVERT: G 161 ASN cc_start: 0.7603 (m-40) cc_final: 0.7298 (t0) REVERT: G 207 TYR cc_start: 0.7410 (t80) cc_final: 0.7105 (t80) REVERT: G 227 ARG cc_start: 0.6632 (ttt180) cc_final: 0.5801 (ttm-80) REVERT: G 371 MET cc_start: 0.5433 (mmm) cc_final: 0.5098 (mtt) REVERT: H 124 TYR cc_start: 0.8258 (m-80) cc_final: 0.7937 (m-80) outliers start: 41 outliers final: 25 residues processed: 161 average time/residue: 0.1343 time to fit residues: 32.7054 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 : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU 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 J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 169 optimal weight: 30.0000 chunk 39 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 106 ASN I 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.110229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.090985 restraints weight = 66838.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090484 restraints weight = 67561.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091300 restraints weight = 55643.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.091425 restraints weight = 43310.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.091538 restraints weight = 39976.981| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17553 Z= 0.098 Angle : 0.548 9.212 24458 Z= 0.266 Chirality : 0.038 0.174 2806 Planarity : 0.004 0.044 2586 Dihedral : 20.101 174.057 4258 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.11 % Allowed : 19.42 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.18), residues: 1705 helix: 0.12 (0.27), residues: 384 sheet: -1.54 (0.27), residues: 323 loop : -2.54 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 212 TYR 0.011 0.001 TYR F 5 PHE 0.011 0.001 PHE D 144 TRP 0.006 0.001 TRP C 380 HIS 0.007 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00216 (17553) covalent geometry : angle 0.54816 (24458) hydrogen bonds : bond 0.03161 ( 425) hydrogen bonds : angle 4.72075 ( 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 164 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5360 (tpt) cc_final: 0.5093 (tpt) REVERT: G 161 ASN cc_start: 0.7439 (m-40) cc_final: 0.7178 (t0) REVERT: G 207 TYR cc_start: 0.7332 (t80) cc_final: 0.7041 (t80) REVERT: G 227 ARG cc_start: 0.6479 (ttt180) cc_final: 0.5681 (ttm-80) REVERT: G 254 MET cc_start: 0.6045 (mmm) cc_final: 0.5776 (mmm) REVERT: G 371 MET cc_start: 0.5397 (mmm) cc_final: 0.5172 (mtt) REVERT: H 124 TYR cc_start: 0.8212 (m-80) cc_final: 0.7944 (m-80) outliers start: 47 outliers final: 31 residues processed: 155 average time/residue: 0.1248 time to fit residues: 29.7548 Evaluate side-chains 136 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL 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 E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 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 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 85 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 overall best weight: 2.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN I 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.106368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.086350 restraints weight = 66747.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.086106 restraints weight = 61795.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.086668 restraints weight = 58379.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.087066 restraints weight = 42802.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.087141 restraints weight = 39715.491| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17553 Z= 0.140 Angle : 0.597 8.459 24458 Z= 0.296 Chirality : 0.039 0.167 2806 Planarity : 0.004 0.045 2586 Dihedral : 20.151 173.213 4258 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.78 % Allowed : 19.42 % Favored : 76.81 % 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: -2.36 (0.19), residues: 1705 helix: 0.06 (0.27), residues: 386 sheet: -1.33 (0.27), residues: 324 loop : -2.43 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 250 TYR 0.011 0.001 TYR C 273 PHE 0.017 0.001 PHE F 52 TRP 0.013 0.001 TRP B 257 HIS 0.009 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00314 (17553) covalent geometry : angle 0.59749 (24458) hydrogen bonds : bond 0.03639 ( 425) hydrogen bonds : angle 4.89845 ( 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 168 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5303 (tpt) cc_final: 0.4770 (tpt) REVERT: B 250 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7443 (ttt90) REVERT: B 373 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6296 (tp) REVERT: E 79 MET cc_start: 0.6371 (mmt) cc_final: 0.6051 (mmt) REVERT: F 5 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6387 (p90) REVERT: G 136 ILE cc_start: 0.4453 (OUTLIER) cc_final: 0.4158 (mm) REVERT: G 161 ASN cc_start: 0.7665 (m-40) cc_final: 0.7384 (t0) REVERT: G 371 MET cc_start: 0.5409 (mmm) cc_final: 0.5069 (mtt) REVERT: H 124 TYR cc_start: 0.8347 (m-80) cc_final: 0.7971 (m-80) outliers start: 57 outliers final: 38 residues processed: 157 average time/residue: 0.1233 time to fit residues: 29.7802 Evaluate side-chains 141 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU 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 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 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 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 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 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 I residue 90 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.087316 restraints weight = 66132.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.087028 restraints weight = 66672.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.087635 restraints weight = 59240.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088018 restraints weight = 42514.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.088109 restraints weight = 40105.121| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17553 Z= 0.134 Angle : 0.593 9.284 24458 Z= 0.291 Chirality : 0.039 0.161 2806 Planarity : 0.004 0.045 2586 Dihedral : 20.184 175.732 4258 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.98 % Allowed : 20.21 % Favored : 75.81 % 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: 0.16 (0.27), residues: 386 sheet: -1.14 (0.28), residues: 319 loop : -2.32 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 250 TYR 0.009 0.001 TYR G 323 PHE 0.011 0.001 PHE C 59 TRP 0.014 0.001 TRP B 257 HIS 0.009 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00301 (17553) covalent geometry : angle 0.59346 (24458) hydrogen bonds : bond 0.03388 ( 425) hydrogen bonds : angle 4.86464 ( 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 163 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 103 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5264 (mtp) REVERT: B 235 MET cc_start: 0.5028 (tpt) cc_final: 0.4397 (tpp) REVERT: B 373 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6283 (tp) REVERT: C 54 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7274 (pt) REVERT: C 391 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (mm) REVERT: D 133 MET cc_start: 0.6077 (mmt) cc_final: 0.5824 (mmt) REVERT: E 31 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5696 (tp40) REVERT: E 79 MET cc_start: 0.6496 (mmt) cc_final: 0.6288 (mmt) REVERT: F 5 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6469 (p90) REVERT: G 136 ILE cc_start: 0.4610 (OUTLIER) cc_final: 0.4313 (mm) REVERT: G 227 ARG cc_start: 0.6598 (ttt180) cc_final: 0.5700 (ttm-80) REVERT: G 371 MET cc_start: 0.5229 (mmm) cc_final: 0.4834 (mtt) REVERT: H 124 TYR cc_start: 0.8232 (m-80) cc_final: 0.7816 (m-80) outliers start: 60 outliers final: 45 residues processed: 151 average time/residue: 0.1256 time to fit residues: 29.2633 Evaluate side-chains 146 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 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 391 LEU 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 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 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 143 VAL 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 327 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN E 132 HIS G 259 HIS G 276 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.100300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080699 restraints weight = 68080.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.080257 restraints weight = 68959.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080910 restraints weight = 64357.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081210 restraints weight = 46704.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.081263 restraints weight = 44578.581| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17553 Z= 0.270 Angle : 0.866 20.208 24458 Z= 0.431 Chirality : 0.048 0.228 2806 Planarity : 0.007 0.056 2586 Dihedral : 20.725 172.408 4258 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.04 % Allowed : 21.40 % Favored : 73.56 % 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: -2.79 (0.18), residues: 1705 helix: -0.84 (0.25), residues: 385 sheet: -1.14 (0.31), residues: 288 loop : -2.60 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 347 TYR 0.027 0.003 TYR H 124 PHE 0.025 0.003 PHE C 59 TRP 0.027 0.003 TRP G 380 HIS 0.016 0.002 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00607 (17553) covalent geometry : angle 0.86603 (24458) hydrogen bonds : bond 0.05838 ( 425) hydrogen bonds : angle 5.82558 ( 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 180 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 104 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 373 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6456 (tp) REVERT: C 301 MET cc_start: 0.8387 (tmm) cc_final: 0.7588 (tmm) REVERT: C 332 GLU cc_start: 0.6769 (tp30) cc_final: 0.6541 (pm20) REVERT: D 133 MET cc_start: 0.6512 (mmt) cc_final: 0.6233 (mmt) REVERT: F 5 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6299 (p90) REVERT: G 371 MET cc_start: 0.5303 (mmm) cc_final: 0.4974 (mtt) outliers start: 76 outliers final: 52 residues processed: 169 average time/residue: 0.1139 time to fit residues: 30.5509 Evaluate side-chains 150 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 ILE 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 338 THR 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 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 132 HIS 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 213 LEU 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 84 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP 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: 1.9990 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS G 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.104566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.084816 restraints weight = 66655.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084588 restraints weight = 61731.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.085181 restraints weight = 57475.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.085537 restraints weight = 41090.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.085657 restraints weight = 38578.034| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17553 Z= 0.112 Angle : 0.627 19.065 24458 Z= 0.304 Chirality : 0.040 0.164 2806 Planarity : 0.004 0.056 2586 Dihedral : 20.446 171.035 4258 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.45 % Allowed : 23.92 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.19), residues: 1705 helix: -0.18 (0.27), residues: 386 sheet: -0.81 (0.31), residues: 289 loop : -2.35 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 171 TYR 0.014 0.001 TYR H 124 PHE 0.010 0.001 PHE G 59 TRP 0.013 0.001 TRP C 271 HIS 0.016 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00249 (17553) covalent geometry : angle 0.62669 (24458) hydrogen bonds : bond 0.03439 ( 425) hydrogen bonds : angle 5.06362 ( 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 147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4656 (mtp) REVERT: C 382 LEU cc_start: 0.6900 (tp) cc_final: 0.6687 (tp) REVERT: C 391 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7786 (mm) REVERT: E 99 GLU cc_start: 0.7115 (pp20) cc_final: 0.6643 (mm-30) REVERT: F 5 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6628 (p90) REVERT: G 227 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5640 (ttm110) REVERT: G 350 MET cc_start: 0.7119 (ptm) cc_final: 0.6817 (ptm) REVERT: G 371 MET cc_start: 0.5439 (mmm) cc_final: 0.5217 (mtt) REVERT: J 23 MET cc_start: 0.5702 (tpp) cc_final: 0.5461 (tpp) outliers start: 37 outliers final: 27 residues processed: 138 average time/residue: 0.1192 time to fit residues: 25.4754 Evaluate side-chains 124 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 391 LEU 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 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 G residue 169 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS G 259 HIS ** 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 = 0.4225 r_free = 0.4225 target = 0.101857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082139 restraints weight = 67222.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.081928 restraints weight = 59765.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.082289 restraints weight = 66344.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.082510 restraints weight = 46575.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.082634 restraints weight = 42512.889| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17553 Z= 0.186 Angle : 0.696 17.681 24458 Z= 0.341 Chirality : 0.042 0.187 2806 Planarity : 0.005 0.050 2586 Dihedral : 20.532 165.024 4258 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.72 % Allowed : 24.32 % Favored : 72.96 % 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: -2.39 (0.19), residues: 1705 helix: -0.40 (0.26), residues: 385 sheet: -1.11 (0.30), residues: 305 loop : -2.32 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 171 TYR 0.014 0.002 TYR G 86 PHE 0.017 0.002 PHE D 144 TRP 0.020 0.002 TRP G 380 HIS 0.013 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00425 (17553) covalent geometry : angle 0.69553 (24458) hydrogen bonds : bond 0.04326 ( 425) hydrogen bonds : angle 5.25784 ( 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 146 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.5344 (OUTLIER) cc_final: 0.4647 (ttp) REVERT: C 332 GLU cc_start: 0.6656 (tp30) cc_final: 0.6349 (pm20) REVERT: C 391 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7765 (pp) REVERT: E 128 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.4036 (ttp) REVERT: F 5 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6062 (p90) REVERT: G 227 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5554 (ttm110) REVERT: G 316 MET cc_start: 0.7122 (mmt) cc_final: 0.6757 (mmt) REVERT: G 371 MET cc_start: 0.5319 (mmm) cc_final: 0.4977 (mtt) outliers start: 41 outliers final: 33 residues processed: 135 average time/residue: 0.1195 time to fit residues: 25.5731 Evaluate side-chains 139 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 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 391 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS G 259 HIS ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.103822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.083962 restraints weight = 66584.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.083871 restraints weight = 55403.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.084337 restraints weight = 53875.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084495 restraints weight = 40276.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.084588 restraints weight = 38378.505| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17553 Z= 0.111 Angle : 0.621 17.507 24458 Z= 0.302 Chirality : 0.040 0.156 2806 Planarity : 0.004 0.045 2586 Dihedral : 20.458 162.021 4258 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.58 % Allowed : 24.19 % Favored : 73.23 % 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: -2.19 (0.19), residues: 1705 helix: -0.12 (0.27), residues: 385 sheet: -0.81 (0.30), residues: 308 loop : -2.31 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 171 TYR 0.010 0.001 TYR H 124 PHE 0.010 0.001 PHE C 91 TRP 0.012 0.001 TRP C 271 HIS 0.014 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00251 (17553) covalent geometry : angle 0.62118 (24458) hydrogen bonds : bond 0.03379 ( 425) hydrogen bonds : angle 4.99159 ( 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 139 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4492 (mtp) REVERT: B 235 MET cc_start: 0.4782 (tpt) cc_final: 0.4132 (tpt) REVERT: C 391 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7748 (pp) REVERT: E 79 MET cc_start: 0.7202 (mtp) cc_final: 0.6991 (ptp) REVERT: E 99 GLU cc_start: 0.7101 (pp20) cc_final: 0.6622 (mm-30) REVERT: F 5 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5944 (p90) REVERT: G 227 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5631 (ttm110) REVERT: G 350 MET cc_start: 0.6874 (ptm) cc_final: 0.6598 (ptt) REVERT: G 371 MET cc_start: 0.5658 (mmm) cc_final: 0.5448 (mtt) REVERT: J 23 MET cc_start: 0.5560 (tpp) cc_final: 0.5343 (tpp) outliers start: 39 outliers final: 31 residues processed: 129 average time/residue: 0.1178 time to fit residues: 24.2177 Evaluate side-chains 134 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 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 391 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL 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 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 33 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 52 optimal weight: 0.0370 chunk 85 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 GLN C 296 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN G 259 HIS ** 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 = 0.4307 r_free = 0.4307 target = 0.106046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.086744 restraints weight = 66634.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.086800 restraints weight = 61651.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.087404 restraints weight = 61141.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.087482 restraints weight = 43754.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.087694 restraints weight = 39816.260| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17553 Z= 0.097 Angle : 0.590 15.525 24458 Z= 0.284 Chirality : 0.039 0.161 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.328 163.258 4258 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.45 % Allowed : 24.45 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1705 helix: 0.08 (0.27), residues: 386 sheet: -0.42 (0.31), residues: 289 loop : -2.15 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 171 TYR 0.014 0.001 TYR H 124 PHE 0.012 0.001 PHE D 144 TRP 0.013 0.001 TRP C 52 HIS 0.019 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00216 (17553) covalent geometry : angle 0.58966 (24458) hydrogen bonds : bond 0.02934 ( 425) hydrogen bonds : angle 4.77740 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.45 seconds wall clock time: 40 minutes 3.42 seconds (2403.42 seconds total)