Starting phenix.real_space_refine on Mon Oct 26 12:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfj_25874/10_2026/7tfj_25874.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 370 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 56 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 12880 2.51 5 N 3516 2.21 5 O 4052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3130 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2685 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.65, per 1000 atoms: 0.18 Number of scatterers: 20607 At special positions: 0 Unit cell: (119.232, 122.544, 137.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 18 33.99 S 81 16.00 P 56 15.00 Mg 4 11.99 O 4052 8.00 N 3516 7.00 C 12880 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: 1.93 Conformation dependent library (CDL) restraints added in 944.5 milliseconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 15 sheets defined 50.7% alpha, 14.9% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.521A pdb=" N TYR A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.751A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.572A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.280A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.521A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.508A pdb=" N PHE A 466 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.505A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.369A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.363A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.689A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.186A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.502A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.617A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 668 through 691 removed outlier: 3.663A pdb=" N ARG A 691 " --> pdb=" O HIS A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.538A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.515A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.725A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.880A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.603A pdb=" N TYR C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.572A pdb=" N MET C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.090A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.991A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.562A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.544A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.868A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.606A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.077A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.898A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.548A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.551A pdb=" N GLU D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 39' Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.914A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.339A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.773A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.141A pdb=" N LYS E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.409A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 105 through 119 removed outlier: 3.543A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.016A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.660A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.674A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.976A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 221 Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.122A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.713A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'H' and resid 9 through 19 Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.748A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 215 Processing helix chain 'H' and resid 216 through 221 removed outlier: 4.337A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 352 removed outlier: 8.061A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.923A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.093A pdb=" N LEU B 76 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 114 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 78 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.573A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.924A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.808A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.081A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.511A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 62 removed outlier: 4.350A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 116 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H 163 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MSE H 161 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.124A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.986A pdb=" N VAL F 203 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 102 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.741A pdb=" N VAL G 26 " --> pdb=" O MSE G 70 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR G 136 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'G' and resid 167 through 172 removed outlier: 3.715A pdb=" N ILE G 167 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER G 177 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR H 114 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.546A pdb=" N VAL H 66 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 26 " --> pdb=" O MSE H 70 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 29 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6811 1.37 - 1.52: 8059 1.52 - 1.67: 5998 1.67 - 1.82: 115 1.82 - 1.97: 40 Bond restraints: 21023 Sorted by residual: bond pdb=" C3' DG J 4 " pdb=" C2' DG J 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA J 5 " pdb=" C2' DA J 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 bond pdb=" C3' DA J 16 " pdb=" C2' DA J 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C3' DT I 24 " pdb=" C2' DT I 24 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.98e+00 bond pdb=" C3' DT I 21 " pdb=" C2' DT I 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 ... (remaining 21018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28036 2.07 - 4.14: 475 4.14 - 6.22: 77 6.22 - 8.29: 10 8.29 - 10.36: 3 Bond angle restraints: 28601 Sorted by residual: angle pdb=" N GLU C 307 " pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " ideal model delta sigma weight residual 110.28 118.10 -7.82 1.55e+00 4.16e-01 2.54e+01 angle pdb=" CA ARG E 106 " pdb=" CB ARG E 106 " pdb=" CG ARG E 106 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" N3 DT I 28 " pdb=" C4 DT I 28 " pdb=" O4 DT I 28 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT J 19 " pdb=" C4 DT J 19 " pdb=" O4 DT J 19 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I 10 " pdb=" C4 DT I 10 " pdb=" O4 DT I 10 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 28596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 12291 30.79 - 61.58: 464 61.58 - 92.37: 22 92.37 - 123.17: 1 123.17 - 153.96: 2 Dihedral angle restraints: 12780 sinusoidal: 5516 harmonic: 7264 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.91 118.91 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 86.23 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C4' DT J 19 " pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " pdb=" P DA J 20 " ideal model delta sinusoidal sigma weight residual 220.00 85.93 134.07 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 12777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2255 0.037 - 0.075: 788 0.075 - 0.112: 231 0.112 - 0.150: 50 0.150 - 0.187: 6 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASP D 178 " pdb=" N ASP D 178 " pdb=" C ASP D 178 " pdb=" CB ASP D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PHE H 19 " pdb=" N PHE H 19 " pdb=" C PHE H 19 " pdb=" CB PHE H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB THR H 193 " pdb=" CA THR H 193 " pdb=" OG1 THR H 193 " pdb=" CG2 THR H 193 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3327 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 251 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO H 252 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO H 252 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO H 252 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.061 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO E 63 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 680 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TYR A 680 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 680 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 681 " 0.014 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 302 2.65 - 3.21: 18898 3.21 - 3.78: 31952 3.78 - 4.34: 43913 4.34 - 4.90: 72576 Nonbonded interactions: 167641 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.088 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.142 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.151 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.164 2.170 ... (remaining 167636 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 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.700 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21023 Z= 0.209 Angle : 0.645 10.361 28601 Z= 0.378 Chirality : 0.042 0.187 3330 Planarity : 0.005 0.132 3483 Dihedral : 14.908 153.957 8052 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.17), residues: 2466 helix: 1.09 (0.16), residues: 1127 sheet: -0.35 (0.25), residues: 469 loop : -0.77 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 80 TYR 0.016 0.001 TYR A 596 PHE 0.028 0.001 PHE A 335 TRP 0.016 0.002 TRP A 543 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.21 (21023) covalent geometry : angle 0.64451 / 0.38 (28601) hydrogen bonds : bond 0.18187 / 11.91 ( 1063) hydrogen bonds : angle 6.93227 / 4.91 ( 3040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7704 (pm20) cc_final: 0.6718 (tt0) REVERT: A 399 MET cc_start: 0.7742 (ppp) cc_final: 0.7038 (ppp) REVERT: A 414 LEU cc_start: 0.7176 (mm) cc_final: 0.6862 (mm) REVERT: A 660 MET cc_start: 0.7036 (mtm) cc_final: 0.6800 (ttm) REVERT: A 666 PHE cc_start: 0.6949 (t80) cc_final: 0.6279 (t80) REVERT: D 115 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7303 (ttp-170) REVERT: E 258 ASP cc_start: 0.7952 (p0) cc_final: 0.7742 (p0) REVERT: G 149 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8055 (mtm180) REVERT: G 228 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7847 (mtt90) REVERT: H 215 ILE cc_start: 0.7806 (pt) cc_final: 0.7526 (pt) REVERT: H 238 GLN cc_start: 0.7922 (tt0) cc_final: 0.6981 (tm-30) outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.1485 time to fit residues: 84.1713 Evaluate side-chains 283 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS B 108 HIS B 146 GLN C 184 HIS ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118620 restraints weight = 26933.765| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.61 r_work: 0.3336 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21023 Z= 0.270 Angle : 0.670 10.667 28601 Z= 0.351 Chirality : 0.045 0.231 3330 Planarity : 0.005 0.078 3483 Dihedral : 13.825 138.567 3164 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.59 % Allowed : 8.43 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.17), residues: 2466 helix: 1.12 (0.16), residues: 1145 sheet: -0.33 (0.25), residues: 465 loop : -0.65 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 80 TYR 0.022 0.002 TYR B 186 PHE 0.016 0.002 PHE F 248 TRP 0.013 0.002 TRP A 323 HIS 0.013 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (21023) covalent geometry : angle 0.66982 / 0.35 (28601) hydrogen bonds : bond 0.05347 / 3.56 ( 1063) hydrogen bonds : angle 5.21058 / 3.72 ( 3040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7990 (pm20) cc_final: 0.6919 (tt0) REVERT: A 399 MET cc_start: 0.7652 (ppp) cc_final: 0.5741 (mtt) REVERT: A 591 MET cc_start: 0.7685 (tpp) cc_final: 0.7456 (tpp) REVERT: A 666 PHE cc_start: 0.7522 (t80) cc_final: 0.6715 (t80) REVERT: B 129 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7673 (tpp-160) REVERT: C 140 ASN cc_start: 0.8085 (p0) cc_final: 0.7794 (p0) REVERT: C 307 GLU cc_start: 0.7272 (mp0) cc_final: 0.6784 (mp0) REVERT: D 282 GLU cc_start: 0.8187 (tt0) cc_final: 0.7925 (tt0) REVERT: E 95 GLU cc_start: 0.8244 (mp0) cc_final: 0.7972 (mp0) REVERT: F 163 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7958 (p) REVERT: G 55 GLU cc_start: 0.8311 (mp0) cc_final: 0.8088 (tm-30) REVERT: G 149 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8193 (mtm110) REVERT: G 223 ASP cc_start: 0.6561 (p0) cc_final: 0.6068 (p0) REVERT: H 14 ARG cc_start: 0.8877 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: H 61 ARG cc_start: 0.6846 (ttm170) cc_final: 0.6015 (ptt90) REVERT: H 174 ASP cc_start: 0.7263 (t70) cc_final: 0.7025 (t0) outliers start: 35 outliers final: 25 residues processed: 335 average time/residue: 0.1613 time to fit residues: 81.0904 Evaluate side-chains 309 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain H residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [216, 187, 43, 3, 177, 172, 85, 117, 122, 140, 171] chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 HIS C 83 ASN D 124 HIS ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS H 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120167 restraints weight = 26965.695| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.63 r_work: 0.3367 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21023 Z= 0.149 Angle : 0.570 11.409 28601 Z= 0.299 Chirality : 0.041 0.230 3330 Planarity : 0.004 0.060 3483 Dihedral : 13.913 134.321 3161 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.72 % Allowed : 11.51 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.17), residues: 2466 helix: 1.35 (0.16), residues: 1150 sheet: -0.35 (0.24), residues: 479 loop : -0.58 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 175 TYR 0.021 0.001 TYR B 186 PHE 0.022 0.002 PHE G 169 TRP 0.010 0.001 TRP A 543 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (21023) covalent geometry : angle 0.56958 / 0.30 (28601) hydrogen bonds : bond 0.04577 / 3.04 ( 1063) hydrogen bonds : angle 4.85257 / 3.45 ( 3040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 305 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7997 (pm20) cc_final: 0.6921 (tt0) REVERT: A 399 MET cc_start: 0.7532 (ppp) cc_final: 0.5590 (mtt) REVERT: B 129 ARG cc_start: 0.8077 (tpp-160) cc_final: 0.7464 (tpp-160) REVERT: B 133 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7649 (mt) REVERT: B 154 LEU cc_start: 0.8191 (mt) cc_final: 0.7761 (mm) REVERT: B 158 CYS cc_start: 0.7745 (m) cc_final: 0.7503 (m) REVERT: C 17 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: C 140 ASN cc_start: 0.8048 (p0) cc_final: 0.7766 (p0) REVERT: C 307 GLU cc_start: 0.7237 (mp0) cc_final: 0.6920 (mp0) REVERT: G 149 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8232 (mtm110) REVERT: G 223 ASP cc_start: 0.6468 (p0) cc_final: 0.5988 (p0) REVERT: H 14 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: H 61 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6133 (ptt90) REVERT: H 174 ASP cc_start: 0.7329 (t70) cc_final: 0.7128 (t0) REVERT: H 238 GLN cc_start: 0.8097 (tt0) cc_final: 0.6962 (tm-30) outliers start: 38 outliers final: 25 residues processed: 324 average time/residue: 0.1602 time to fit residues: 78.3628 Evaluate side-chains 307 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [236, 62, 212, 137, 238, 171, 191, 97, 158, 35, 160] chunk 236 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 chunk 238 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN F 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121610 restraints weight = 26898.759| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.63 r_work: 0.3380 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21023 Z= 0.130 Angle : 0.554 10.314 28601 Z= 0.288 Chirality : 0.040 0.225 3330 Planarity : 0.004 0.051 3483 Dihedral : 13.911 134.369 3161 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.09 % Allowed : 12.83 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.17), residues: 2466 helix: 1.51 (0.16), residues: 1146 sheet: -0.38 (0.23), residues: 494 loop : -0.54 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 175 TYR 0.022 0.001 TYR B 186 PHE 0.027 0.001 PHE G 169 TRP 0.009 0.001 TRP A 543 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21023) covalent geometry : angle 0.55350 / 0.29 (28601) hydrogen bonds : bond 0.04131 / 2.74 ( 1063) hydrogen bonds : angle 4.61720 / 3.28 ( 3040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 399 MET cc_start: 0.7450 (ppp) cc_final: 0.5509 (mtt) REVERT: A 663 ARG cc_start: 0.4073 (tpt90) cc_final: 0.3751 (tmt-80) REVERT: B 129 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7322 (tpp-160) REVERT: B 133 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7377 (mp) REVERT: B 158 CYS cc_start: 0.7683 (m) cc_final: 0.7366 (m) REVERT: C 17 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: C 69 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 140 ASN cc_start: 0.8035 (p0) cc_final: 0.7509 (p0) REVERT: C 307 GLU cc_start: 0.7130 (mp0) cc_final: 0.6879 (mp0) REVERT: D 115 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7785 (ttp-170) REVERT: G 149 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8243 (mtm110) REVERT: G 223 ASP cc_start: 0.6390 (p0) cc_final: 0.5949 (p0) REVERT: H 14 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8179 (mtm180) REVERT: H 61 ARG cc_start: 0.6806 (ttm170) cc_final: 0.6208 (ptt90) REVERT: H 174 ASP cc_start: 0.7402 (t70) cc_final: 0.7187 (t0) REVERT: H 238 GLN cc_start: 0.8006 (tt0) cc_final: 0.6949 (tm-30) outliers start: 46 outliers final: 35 residues processed: 319 average time/residue: 0.1528 time to fit residues: 74.3911 Evaluate side-chains 312 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [142, 2, 106, 4, 223, 141, 113, 210, 219, 236, 17] chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119681 restraints weight = 26860.009| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.63 r_work: 0.3351 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21023 Z= 0.170 Angle : 0.565 9.617 28601 Z= 0.293 Chirality : 0.041 0.236 3330 Planarity : 0.004 0.046 3483 Dihedral : 13.982 135.081 3161 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 13.37 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.17), residues: 2466 helix: 1.51 (0.16), residues: 1147 sheet: -0.40 (0.23), residues: 496 loop : -0.53 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.023 0.001 TYR B 186 PHE 0.025 0.002 PHE G 169 TRP 0.008 0.001 TRP B 257 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (21023) covalent geometry : angle 0.56478 / 0.29 (28601) hydrogen bonds : bond 0.04231 / 2.81 ( 1063) hydrogen bonds : angle 4.50609 / 3.20 ( 3040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7453 (ppp) cc_final: 0.5557 (mtt) REVERT: A 623 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 129 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.7352 (tpp-160) REVERT: B 133 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 17 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: C 140 ASN cc_start: 0.8080 (p0) cc_final: 0.7822 (p0) REVERT: C 307 GLU cc_start: 0.7212 (mp0) cc_final: 0.6938 (mp0) REVERT: D 322 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (tt) REVERT: G 149 ARG cc_start: 0.8623 (mtm110) cc_final: 0.8230 (mtm110) REVERT: G 199 MSE cc_start: 0.6526 (tpp) cc_final: 0.4496 (mmm) REVERT: G 223 ASP cc_start: 0.6413 (p0) cc_final: 0.5980 (p0) REVERT: G 228 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8027 (mtt-85) REVERT: H 61 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6165 (ptt90) REVERT: H 174 ASP cc_start: 0.7467 (t70) cc_final: 0.7222 (t0) REVERT: H 238 GLN cc_start: 0.8035 (tt0) cc_final: 0.6927 (tm-30) outliers start: 50 outliers final: 38 residues processed: 322 average time/residue: 0.1528 time to fit residues: 75.1328 Evaluate side-chains 317 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [11, 102, 94, 1, 98, 75, 34, 203, 185, 211, 92] chunk 11 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 378 ASN E 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.161052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120114 restraints weight = 26974.416| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.62 r_work: 0.3367 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21023 Z= 0.133 Angle : 0.541 9.711 28601 Z= 0.282 Chirality : 0.040 0.232 3330 Planarity : 0.004 0.046 3483 Dihedral : 13.948 134.874 3161 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.27 % Allowed : 14.19 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.17), residues: 2466 helix: 1.62 (0.16), residues: 1143 sheet: -0.39 (0.23), residues: 502 loop : -0.52 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 175 TYR 0.025 0.001 TYR B 186 PHE 0.025 0.001 PHE G 169 TRP 0.008 0.001 TRP A 543 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21023) covalent geometry : angle 0.54096 / 0.28 (28601) hydrogen bonds : bond 0.03959 / 2.63 ( 1063) hydrogen bonds : angle 4.41167 / 3.14 ( 3040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7411 (ppp) cc_final: 0.5528 (mtt) REVERT: A 623 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 628 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 129 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7843 (tpp-160) REVERT: C 17 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: C 69 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 140 ASN cc_start: 0.8043 (p0) cc_final: 0.7840 (p0) REVERT: C 307 GLU cc_start: 0.7140 (mp0) cc_final: 0.6937 (mp0) REVERT: D 322 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8382 (tt) REVERT: E 68 LEU cc_start: 0.8238 (mm) cc_final: 0.8013 (mm) REVERT: F 24 GLN cc_start: 0.7821 (mp10) cc_final: 0.7612 (mp10) REVERT: G 149 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8247 (mtm110) REVERT: G 223 ASP cc_start: 0.6429 (p0) cc_final: 0.6031 (p0) REVERT: G 228 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8007 (mtt-85) REVERT: H 61 ARG cc_start: 0.6876 (ttm170) cc_final: 0.6174 (ptt90) REVERT: H 79 LEU cc_start: 0.8664 (mp) cc_final: 0.8048 (mt) REVERT: H 238 GLN cc_start: 0.8042 (tt0) cc_final: 0.7016 (tm-30) outliers start: 50 outliers final: 38 residues processed: 332 average time/residue: 0.1503 time to fit residues: 76.4645 Evaluate side-chains 317 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [120, 76, 5, 154, 219, 97, 246, 122, 212, 167, 20] chunk 120 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117525 restraints weight = 27167.621| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.62 r_work: 0.3322 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21023 Z= 0.228 Angle : 0.603 8.751 28601 Z= 0.312 Chirality : 0.042 0.250 3330 Planarity : 0.004 0.048 3483 Dihedral : 14.063 135.883 3161 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.77 % Allowed : 14.78 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.17), residues: 2466 helix: 1.42 (0.16), residues: 1148 sheet: -0.43 (0.23), residues: 507 loop : -0.55 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 80 TYR 0.026 0.002 TYR B 186 PHE 0.024 0.002 PHE A 335 TRP 0.012 0.002 TRP C 15 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (21023) covalent geometry : angle 0.60318 / 0.31 (28601) hydrogen bonds : bond 0.04403 / 2.93 ( 1063) hydrogen bonds : angle 4.48667 / 3.19 ( 3040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7449 (ppp) cc_final: 0.5458 (mtt) REVERT: A 594 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6420 (tp30) REVERT: A 623 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (mt) REVERT: C 17 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: C 307 GLU cc_start: 0.7259 (mp0) cc_final: 0.6907 (mp0) REVERT: D 322 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8412 (tt) REVERT: G 149 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8055 (mtm110) REVERT: G 223 ASP cc_start: 0.6438 (p0) cc_final: 0.6019 (p0) REVERT: H 61 ARG cc_start: 0.6883 (ttm170) cc_final: 0.6160 (ptt90) REVERT: H 238 GLN cc_start: 0.8117 (tt0) cc_final: 0.7073 (tm-30) outliers start: 61 outliers final: 47 residues processed: 319 average time/residue: 0.1598 time to fit residues: 77.3302 Evaluate side-chains 319 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [241, 185, 118, 95, 154, 36, 214, 76, 135, 0, 75] chunk 241 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 36 optimal weight: 0.0040 chunk 214 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN D 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.161248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120441 restraints weight = 27122.185| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.63 r_work: 0.3371 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21023 Z= 0.118 Angle : 0.551 9.686 28601 Z= 0.285 Chirality : 0.040 0.235 3330 Planarity : 0.004 0.047 3483 Dihedral : 13.951 134.882 3161 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.90 % Allowed : 16.14 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.17), residues: 2466 helix: 1.65 (0.16), residues: 1142 sheet: -0.39 (0.23), residues: 508 loop : -0.51 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.025 0.001 TYR B 186 PHE 0.027 0.001 PHE G 169 TRP 0.011 0.001 TRP C 15 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21023) covalent geometry : angle 0.55100 / 0.29 (28601) hydrogen bonds : bond 0.03851 / 2.56 ( 1063) hydrogen bonds : angle 4.32043 / 3.07 ( 3040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.7856 (mt) cc_final: 0.7334 (tt) REVERT: A 399 MET cc_start: 0.7372 (ppp) cc_final: 0.5497 (mtt) REVERT: A 445 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7697 (ttp-110) REVERT: A 471 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6688 (tt) REVERT: A 564 TYR cc_start: 0.7947 (m-10) cc_final: 0.7680 (m-10) REVERT: A 594 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6339 (tp30) REVERT: A 623 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 628 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 129 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: C 17 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: C 69 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 149 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8274 (mtm110) REVERT: G 223 ASP cc_start: 0.6422 (p0) cc_final: 0.6022 (p0) REVERT: H 1 MSE cc_start: 0.2774 (mmm) cc_final: 0.2268 (tpp) REVERT: H 14 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8321 (mtm-85) REVERT: H 238 GLN cc_start: 0.8045 (tt0) cc_final: 0.7012 (tm-30) outliers start: 42 outliers final: 32 residues processed: 316 average time/residue: 0.1556 time to fit residues: 75.0853 Evaluate side-chains 315 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [212, 85, 127, 84, 101, 49, 211, 17, 166, 53, 135] chunk 212 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121275 restraints weight = 27105.829| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.66 r_work: 0.3360 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21023 Z= 0.150 Angle : 0.564 9.356 28601 Z= 0.291 Chirality : 0.041 0.236 3330 Planarity : 0.004 0.049 3483 Dihedral : 13.963 135.490 3161 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.09 % Allowed : 16.27 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.17), residues: 2466 helix: 1.64 (0.16), residues: 1140 sheet: -0.35 (0.23), residues: 508 loop : -0.50 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.026 0.001 TYR B 186 PHE 0.027 0.001 PHE G 169 TRP 0.018 0.002 TRP A 543 HIS 0.009 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (21023) covalent geometry : angle 0.56432 / 0.29 (28601) hydrogen bonds : bond 0.03954 / 2.62 ( 1063) hydrogen bonds : angle 4.31668 / 3.07 ( 3040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 283 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7377 (ppp) cc_final: 0.5495 (mtt) REVERT: A 445 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7647 (ttp-110) REVERT: A 471 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6708 (tt) REVERT: A 564 TYR cc_start: 0.7901 (m-10) cc_final: 0.7645 (m-10) REVERT: A 594 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: A 623 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8453 (mt) REVERT: C 17 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: C 69 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8270 (tm-30) REVERT: D 322 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8339 (tt) REVERT: G 149 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8272 (mtm110) REVERT: G 223 ASP cc_start: 0.6529 (p0) cc_final: 0.6116 (p0) REVERT: H 1 MSE cc_start: 0.3024 (mmm) cc_final: 0.2490 (tpp) REVERT: H 14 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8322 (mtm-85) REVERT: H 238 GLN cc_start: 0.8040 (tt0) cc_final: 0.7021 (tm-30) outliers start: 46 outliers final: 36 residues processed: 319 average time/residue: 0.1532 time to fit residues: 74.9213 Evaluate side-chains 316 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [81, 26, 98, 52, 218, 208, 178, 185, 71, 179, 0] chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 179 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.161441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122132 restraints weight = 27293.250| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.66 r_work: 0.3373 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21023 Z= 0.131 Angle : 0.555 9.597 28601 Z= 0.287 Chirality : 0.041 0.228 3330 Planarity : 0.004 0.047 3483 Dihedral : 13.917 135.193 3161 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.81 % Allowed : 16.55 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.17), residues: 2466 helix: 1.67 (0.16), residues: 1141 sheet: -0.35 (0.23), residues: 508 loop : -0.51 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.025 0.001 TYR B 186 PHE 0.026 0.001 PHE G 169 TRP 0.012 0.001 TRP A 543 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21023) covalent geometry : angle 0.55476 / 0.29 (28601) hydrogen bonds : bond 0.03840 / 2.54 ( 1063) hydrogen bonds : angle 4.26442 / 3.03 ( 3040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8489 (p0) cc_final: 0.8214 (p0) REVERT: A 370 LEU cc_start: 0.7815 (mt) cc_final: 0.7345 (tt) REVERT: A 399 MET cc_start: 0.7274 (ppp) cc_final: 0.5370 (mtt) REVERT: A 445 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7670 (ttp-110) REVERT: A 471 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6634 (tt) REVERT: A 564 TYR cc_start: 0.7869 (m-10) cc_final: 0.7628 (m-10) REVERT: A 594 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6199 (tp30) REVERT: A 623 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 663 ARG cc_start: 0.4225 (tpt90) cc_final: 0.3833 (tmt-80) REVERT: C 17 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: C 69 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 322 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8345 (tt) REVERT: E 68 LEU cc_start: 0.8219 (mm) cc_final: 0.7957 (mm) REVERT: G 149 ARG cc_start: 0.8614 (mtm110) cc_final: 0.8277 (mtm110) REVERT: G 223 ASP cc_start: 0.6518 (p0) cc_final: 0.6102 (p0) REVERT: H 14 ARG cc_start: 0.8954 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: H 61 ARG cc_start: 0.5963 (mtm110) cc_final: 0.5722 (mtm110) REVERT: H 238 GLN cc_start: 0.8021 (tt0) cc_final: 0.6976 (tm-30) outliers start: 40 outliers final: 32 residues processed: 310 average time/residue: 0.1535 time to fit residues: 72.3623 Evaluate side-chains 315 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [63, 116, 0, 25, 132, 183, 70, 1, 23, 35, 158] chunk 63 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 158 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122291 restraints weight = 27291.057| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.63 r_work: 0.3389 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21023 Z= 0.124 Angle : 0.561 9.669 28601 Z= 0.289 Chirality : 0.042 0.481 3330 Planarity : 0.004 0.047 3483 Dihedral : 13.887 135.090 3161 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.99 % Allowed : 16.32 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.17), residues: 2466 helix: 1.71 (0.16), residues: 1140 sheet: -0.33 (0.23), residues: 507 loop : -0.52 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.026 0.001 TYR B 186 PHE 0.026 0.001 PHE G 169 TRP 0.012 0.001 TRP A 543 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21023) covalent geometry : angle 0.56053 / 0.29 (28601) hydrogen bonds : bond 0.03753 / 2.48 ( 1063) hydrogen bonds : angle 4.21777 / 3.00 ( 3040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4734.98 seconds wall clock time: 82 minutes 2.20 seconds (4922.20 seconds total)