Starting phenix.real_space_refine on Wed Jun 18 10:19:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfj_25874/06_2025/7tfj_25874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfj_25874/06_2025/7tfj_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_25874/06_2025/7tfj_25874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfj_25874/06_2025/7tfj_25874.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfj_25874/06_2025/7tfj_25874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfj_25874/06_2025/7tfj_25874.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.36, per 1000 atoms: 0.55 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: 5.32 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 8.22 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: 7.40 Time building geometry restraints manager: 6.17 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=" N GLU B 287 " pdb=" CA GLU B 287 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.94e+00 bond pdb=" CG GLU C 307 " pdb=" CD GLU C 307 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" N GLN E 110 " pdb=" CA GLN E 110 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.20e+00 bond pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.49e-02 4.50e+03 3.69e+00 bond pdb=" C LYS A 550 " pdb=" N PRO A 551 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 3.01e+00 ... (remaining 21018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28093 2.07 - 4.14: 419 4.14 - 6.22: 76 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=" CA GLU C 307 " pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.23 3.73 1.00e+00 1.00e+00 1.39e+01 angle pdb=" C GLU A 293 " pdb=" N GLU A 294 " pdb=" CA GLU A 294 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 ... (remaining 28596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 12302 30.79 - 61.58: 497 61.58 - 92.37: 22 92.37 - 123.17: 1 123.17 - 153.96: 2 Dihedral angle restraints: 12824 sinusoidal: 5560 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 12821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2314 0.037 - 0.075: 759 0.075 - 0.112: 204 0.112 - 0.150: 48 0.150 - 0.187: 5 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.860 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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= 0.145 Angle : 0.627 10.361 28601 Z= 0.333 Chirality : 0.041 0.187 3330 Planarity : 0.005 0.132 3483 Dihedral : 15.192 153.957 8096 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 543 HIS 0.004 0.001 HIS B 232 PHE 0.028 0.001 PHE A 335 TYR 0.016 0.001 TYR A 596 ARG 0.011 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.18187 ( 1063) hydrogen bonds : angle 6.93227 ( 3040) covalent geometry : bond 0.00319 (21023) covalent geometry : angle 0.62725 (28601) *********************** 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 : 2.477 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: 0.7037 (ppp) REVERT: A 414 LEU cc_start: 0.7176 (mm) cc_final: 0.6861 (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: 0.8056 (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: 0.3318 time to fit residues: 185.8368 Evaluate side-chains 284 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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: chunk 211 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS B 146 GLN C 184 HIS D 124 HIS ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122983 restraints weight = 26889.764| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.63 r_work: 0.3401 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21023 Z= 0.150 Angle : 0.577 11.880 28601 Z= 0.301 Chirality : 0.041 0.150 3330 Planarity : 0.004 0.081 3483 Dihedral : 14.146 134.873 3208 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.04 % Allowed : 8.30 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2466 helix: 1.36 (0.16), residues: 1145 sheet: -0.21 (0.26), residues: 447 loop : -0.63 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 323 HIS 0.010 0.001 HIS E 93 PHE 0.017 0.001 PHE H 19 TYR 0.020 0.001 TYR B 186 ARG 0.005 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1063) hydrogen bonds : angle 5.00557 ( 3040) covalent geometry : bond 0.00341 (21023) covalent geometry : angle 0.57681 (28601) *********************** 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 342 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7941 (pm20) cc_final: 0.6870 (tt0) REVERT: A 399 MET cc_start: 0.7586 (ppp) cc_final: 0.5553 (mtt) REVERT: A 632 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7374 (mtt-85) REVERT: A 666 PHE cc_start: 0.7425 (t80) cc_final: 0.6570 (t80) REVERT: B 129 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7662 (tpp-160) REVERT: C 140 ASN cc_start: 0.8006 (p0) cc_final: 0.7721 (p0) REVERT: C 307 GLU cc_start: 0.7250 (mp0) cc_final: 0.6921 (mp0) REVERT: D 282 GLU cc_start: 0.8125 (tt0) cc_final: 0.7894 (tt0) REVERT: E 95 GLU cc_start: 0.8120 (mp0) cc_final: 0.7721 (mp0) REVERT: G 149 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8219 (mtm110) REVERT: G 223 ASP cc_start: 0.6531 (p0) cc_final: 0.6059 (p0) REVERT: H 14 ARG cc_start: 0.8877 (mtm-85) cc_final: 0.8204 (mtm180) REVERT: H 61 ARG cc_start: 0.6855 (ttm170) cc_final: 0.6056 (ptt90) REVERT: H 238 GLN cc_start: 0.8069 (tt0) cc_final: 0.6949 (tm-30) outliers start: 23 outliers final: 18 residues processed: 332 average time/residue: 0.3567 time to fit residues: 176.1051 Evaluate side-chains 303 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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 270 SER 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 329 THR 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 G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 2 LEU 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: chunk 64 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 229 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS E 93 HIS G 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.158928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117949 restraints weight = 26584.578| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.59 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21023 Z= 0.238 Angle : 0.614 9.199 28601 Z= 0.319 Chirality : 0.043 0.162 3330 Planarity : 0.004 0.063 3483 Dihedral : 14.356 135.652 3205 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.18 % Allowed : 10.92 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2466 helix: 1.22 (0.15), residues: 1156 sheet: -0.37 (0.24), residues: 482 loop : -0.59 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 257 HIS 0.015 0.001 HIS D 124 PHE 0.024 0.002 PHE A 335 TYR 0.024 0.002 TYR B 186 ARG 0.005 0.001 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 1063) hydrogen bonds : angle 4.81187 ( 3040) covalent geometry : bond 0.00573 (21023) covalent geometry : angle 0.61442 (28601) *********************** 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 342 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7990 (pm20) cc_final: 0.6929 (tt0) REVERT: A 399 MET cc_start: 0.7564 (ppp) cc_final: 0.5687 (mtt) REVERT: B 129 ARG cc_start: 0.8150 (tpp-160) cc_final: 0.7356 (tpp-160) REVERT: B 133 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7489 (mp) REVERT: C 17 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: C 140 ASN cc_start: 0.8122 (p0) cc_final: 0.7840 (p0) REVERT: C 307 GLU cc_start: 0.7282 (mp0) cc_final: 0.6910 (mp0) REVERT: D 282 GLU cc_start: 0.8189 (tt0) cc_final: 0.7962 (tt0) REVERT: F 163 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7987 (p) REVERT: G 149 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8261 (mtm110) REVERT: G 223 ASP cc_start: 0.6541 (p0) cc_final: 0.6077 (p0) REVERT: H 14 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: H 61 ARG cc_start: 0.6836 (ttm170) cc_final: 0.6057 (ptt90) REVERT: H 238 GLN cc_start: 0.8090 (tt0) cc_final: 0.7082 (tm-30) outliers start: 48 outliers final: 37 residues processed: 323 average time/residue: 0.3623 time to fit residues: 175.0086 Evaluate side-chains 315 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 74 THR Chi-restraints excluded: chain D residue 79 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 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 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 MSE Chi-restraints excluded: chain F residue 163 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 55 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 119 optimal weight: 0.0070 chunk 182 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 684 GLN E 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121521 restraints weight = 26956.915| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.63 r_work: 0.3378 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21023 Z= 0.120 Angle : 0.531 10.190 28601 Z= 0.275 Chirality : 0.039 0.138 3330 Planarity : 0.004 0.054 3483 Dihedral : 14.145 135.589 3205 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 12.74 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2466 helix: 1.58 (0.16), residues: 1143 sheet: -0.41 (0.23), residues: 499 loop : -0.47 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.004 0.001 HIS D 124 PHE 0.026 0.001 PHE G 169 TYR 0.023 0.001 TYR B 186 ARG 0.005 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1063) hydrogen bonds : angle 4.45623 ( 3040) covalent geometry : bond 0.00268 (21023) covalent geometry : angle 0.53087 (28601) *********************** 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 342 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 299 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7412 (ppp) cc_final: 0.5468 (mtt) REVERT: A 623 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 628 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 129 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7823 (tpp-160) REVERT: C 17 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: C 69 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 140 ASN cc_start: 0.8039 (p0) cc_final: 0.7779 (p0) REVERT: C 291 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: C 307 GLU cc_start: 0.7077 (mp0) cc_final: 0.6822 (mp0) REVERT: F 163 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7991 (p) REVERT: G 149 ARG cc_start: 0.8634 (mtm110) cc_final: 0.8039 (mtm110) REVERT: G 223 ASP cc_start: 0.6441 (p0) cc_final: 0.5990 (p0) REVERT: H 61 ARG cc_start: 0.6786 (ttm170) cc_final: 0.6128 (ptt90) REVERT: H 79 LEU cc_start: 0.8608 (mp) cc_final: 0.7977 (mt) outliers start: 43 outliers final: 27 residues processed: 326 average time/residue: 0.3879 time to fit residues: 193.0804 Evaluate side-chains 304 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 MET Chi-restraints excluded: chain B residue 239 MET 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 291 GLN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 22 CYS 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 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 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: chunk 204 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 177 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN C 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121620 restraints weight = 26982.399| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.62 r_work: 0.3381 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21023 Z= 0.121 Angle : 0.524 10.224 28601 Z= 0.271 Chirality : 0.039 0.188 3330 Planarity : 0.004 0.049 3483 Dihedral : 14.063 135.293 3205 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 14.01 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2466 helix: 1.74 (0.16), residues: 1135 sheet: -0.35 (0.23), residues: 505 loop : -0.44 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.004 0.001 HIS B 108 PHE 0.027 0.001 PHE G 169 TYR 0.024 0.001 TYR B 186 ARG 0.006 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1063) hydrogen bonds : angle 4.31268 ( 3040) covalent geometry : bond 0.00273 (21023) covalent geometry : angle 0.52354 (28601) *********************** 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 341 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7371 (ppp) cc_final: 0.5455 (mtt) REVERT: A 628 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7617 (tm-30) REVERT: B 129 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7840 (tpp-160) REVERT: C 17 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: C 69 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 140 ASN cc_start: 0.8060 (p0) cc_final: 0.7822 (p0) REVERT: C 307 GLU cc_start: 0.7107 (mp0) cc_final: 0.6879 (mp0) REVERT: F 163 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7976 (p) REVERT: G 149 ARG cc_start: 0.8557 (mtm110) cc_final: 0.8195 (mtm110) REVERT: G 223 ASP cc_start: 0.6470 (p0) cc_final: 0.6055 (p0) REVERT: G 228 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7882 (mtt-85) REVERT: H 14 ARG cc_start: 0.8946 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: H 61 ARG cc_start: 0.6844 (ttm170) cc_final: 0.6117 (ptt90) REVERT: H 79 LEU cc_start: 0.8725 (mp) cc_final: 0.8236 (mt) REVERT: H 238 GLN cc_start: 0.8088 (tt0) cc_final: 0.7009 (tm-30) outliers start: 43 outliers final: 31 residues processed: 325 average time/residue: 0.3351 time to fit residues: 165.3092 Evaluate side-chains 304 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 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 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 C residue 291 GLN Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 124 HIS 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 22 CYS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 163 THR 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 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR 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: chunk 26 optimal weight: 5.9990 chunk 157 optimal weight: 0.0000 chunk 160 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119314 restraints weight = 27111.983| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.62 r_work: 0.3345 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21023 Z= 0.172 Angle : 0.559 9.486 28601 Z= 0.288 Chirality : 0.041 0.200 3330 Planarity : 0.004 0.048 3483 Dihedral : 14.141 135.615 3205 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.36 % Allowed : 14.73 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2466 helix: 1.64 (0.16), residues: 1141 sheet: -0.40 (0.23), residues: 511 loop : -0.46 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 257 HIS 0.004 0.001 HIS B 60 PHE 0.025 0.002 PHE G 169 TYR 0.026 0.002 TYR B 186 ARG 0.007 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1063) hydrogen bonds : angle 4.33191 ( 3040) covalent geometry : bond 0.00407 (21023) covalent geometry : angle 0.55930 (28601) *********************** 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 337 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7368 (ppp) cc_final: 0.5540 (mtt) REVERT: A 594 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: C 17 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: C 132 ARG cc_start: 0.8459 (mmm160) cc_final: 0.8120 (mmm160) REVERT: C 140 ASN cc_start: 0.8146 (p0) cc_final: 0.7945 (p0) REVERT: C 307 GLU cc_start: 0.7228 (mp0) cc_final: 0.6862 (mp0) REVERT: D 322 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (tt) REVERT: F 163 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.8012 (p) REVERT: G 149 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8218 (mtm110) REVERT: G 223 ASP cc_start: 0.6489 (p0) cc_final: 0.6088 (p0) REVERT: H 1 MSE cc_start: 0.2806 (mmm) cc_final: 0.2431 (tpp) REVERT: H 14 ARG cc_start: 0.8951 (mtm-85) cc_final: 0.8316 (mtm-85) REVERT: H 238 GLN cc_start: 0.8110 (tt0) cc_final: 0.7061 (tm-30) outliers start: 52 outliers final: 40 residues processed: 319 average time/residue: 0.3543 time to fit residues: 170.3554 Evaluate side-chains 317 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 103 ILE 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 22 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 146 optimal weight: 0.0370 chunk 246 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120487 restraints weight = 26983.605| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.63 r_work: 0.3360 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21023 Z= 0.138 Angle : 0.539 9.384 28601 Z= 0.278 Chirality : 0.040 0.199 3330 Planarity : 0.004 0.048 3483 Dihedral : 14.089 135.662 3205 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.31 % Allowed : 15.32 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2466 helix: 1.73 (0.16), residues: 1134 sheet: -0.36 (0.23), residues: 511 loop : -0.43 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 323 HIS 0.004 0.001 HIS B 108 PHE 0.023 0.001 PHE A 335 TYR 0.026 0.001 TYR B 186 ARG 0.007 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1063) hydrogen bonds : angle 4.25365 ( 3040) covalent geometry : bond 0.00322 (21023) covalent geometry : angle 0.53868 (28601) *********************** 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: 51 poor density : 286 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7364 (ppp) cc_final: 0.5542 (mtt) REVERT: A 445 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7736 (ttp-110) REVERT: A 471 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6713 (tt) REVERT: A 594 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6217 (tp30) REVERT: C 17 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: C 69 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 132 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8208 (mmm160) REVERT: C 307 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6810 (mp0) REVERT: E 68 LEU cc_start: 0.8066 (mm) cc_final: 0.7797 (mm) REVERT: E 119 MET cc_start: 0.5431 (mmm) cc_final: 0.4877 (mmm) REVERT: F 163 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.8010 (p) REVERT: G 149 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8225 (mtm110) REVERT: G 223 ASP cc_start: 0.6462 (p0) cc_final: 0.6063 (p0) REVERT: H 1 MSE cc_start: 0.3199 (mmm) cc_final: 0.2595 (tpp) REVERT: H 14 ARG cc_start: 0.8937 (mtm-85) cc_final: 0.8308 (mtm-85) REVERT: H 238 GLN cc_start: 0.8128 (tt0) cc_final: 0.7092 (tm-30) outliers start: 51 outliers final: 40 residues processed: 320 average time/residue: 0.3530 time to fit residues: 170.3204 Evaluate side-chains 317 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 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 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 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 C residue 316 ASP 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 329 THR 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 22 CYS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 163 THR 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 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: chunk 186 optimal weight: 0.4980 chunk 154 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121230 restraints weight = 27000.012| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.62 r_work: 0.3380 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21023 Z= 0.118 Angle : 0.530 9.686 28601 Z= 0.274 Chirality : 0.040 0.224 3330 Planarity : 0.004 0.046 3483 Dihedral : 13.988 135.430 3205 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.90 % Allowed : 16.00 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2466 helix: 1.81 (0.16), residues: 1135 sheet: -0.34 (0.23), residues: 516 loop : -0.39 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 15 HIS 0.005 0.001 HIS B 108 PHE 0.017 0.001 PHE G 254 TYR 0.026 0.001 TYR B 186 ARG 0.008 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1063) hydrogen bonds : angle 4.15652 ( 3040) covalent geometry : bond 0.00266 (21023) covalent geometry : angle 0.53050 (28601) *********************** 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 333 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.7898 (mt) cc_final: 0.7401 (tt) REVERT: A 399 MET cc_start: 0.7264 (ppp) cc_final: 0.5329 (mtt) REVERT: A 445 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7738 (ttp-110) REVERT: A 594 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6102 (tp30) REVERT: A 625 ASP cc_start: 0.8483 (t0) cc_final: 0.8259 (t0) REVERT: C 17 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: C 69 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8253 (tm-30) REVERT: C 307 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6897 (mp0) REVERT: D 101 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7950 (mtm110) REVERT: D 322 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8356 (tt) REVERT: E 119 MET cc_start: 0.5469 (mmm) cc_final: 0.4902 (mmm) REVERT: F 163 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7982 (p) REVERT: G 149 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8238 (mtm110) REVERT: G 188 MSE cc_start: 0.5731 (mpp) cc_final: 0.4991 (mpp) REVERT: G 199 MSE cc_start: 0.6669 (tpp) cc_final: 0.4683 (mmm) REVERT: G 223 ASP cc_start: 0.6491 (p0) cc_final: 0.6111 (p0) REVERT: H 14 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8301 (mtm-85) REVERT: H 61 ARG cc_start: 0.6048 (mtm110) cc_final: 0.5802 (mtm110) REVERT: H 238 GLN cc_start: 0.8096 (tt0) cc_final: 0.7074 (tm-30) outliers start: 42 outliers final: 32 residues processed: 319 average time/residue: 0.3514 time to fit residues: 169.3240 Evaluate side-chains 307 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 594 GLU 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 103 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 17 GLU 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 C residue 316 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 124 HIS 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 111 GLU 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 22 CYS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 93 ASP 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 Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 143 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122347 restraints weight = 27333.483| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.64 r_work: 0.3399 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21023 Z= 0.109 Angle : 0.530 10.003 28601 Z= 0.273 Chirality : 0.040 0.309 3330 Planarity : 0.004 0.048 3483 Dihedral : 13.894 135.018 3205 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.63 % Allowed : 16.36 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2466 helix: 1.88 (0.16), residues: 1136 sheet: -0.31 (0.23), residues: 515 loop : -0.39 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 15 HIS 0.005 0.001 HIS B 108 PHE 0.024 0.001 PHE A 335 TYR 0.027 0.001 TYR B 186 ARG 0.008 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1063) hydrogen bonds : angle 4.07844 ( 3040) covalent geometry : bond 0.00240 (21023) covalent geometry : angle 0.52957 (28601) *********************** 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 324 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.7826 (mt) cc_final: 0.7378 (tt) REVERT: A 399 MET cc_start: 0.7179 (ppp) cc_final: 0.5174 (mtt) REVERT: A 445 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7737 (ttp-110) REVERT: A 471 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6722 (tt) REVERT: A 594 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5995 (tp30) REVERT: A 628 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 17 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: C 69 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 101 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7928 (mtm110) REVERT: E 68 LEU cc_start: 0.8074 (mm) cc_final: 0.7802 (mm) REVERT: E 119 MET cc_start: 0.5497 (mmm) cc_final: 0.4924 (mmm) REVERT: F 163 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8006 (p) REVERT: G 149 ARG cc_start: 0.8557 (mtm110) cc_final: 0.8252 (mtm110) REVERT: G 188 MSE cc_start: 0.5702 (mpp) cc_final: 0.4968 (mpp) REVERT: G 199 MSE cc_start: 0.6788 (tpp) cc_final: 0.4689 (mmm) REVERT: G 201 GLN cc_start: 0.8552 (mp10) cc_final: 0.7645 (mp10) REVERT: G 223 ASP cc_start: 0.6517 (p0) cc_final: 0.6141 (p0) REVERT: G 228 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7892 (mtt-85) REVERT: H 14 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8291 (mtm-85) REVERT: H 99 ILE cc_start: 0.8696 (tp) cc_final: 0.8456 (mt) REVERT: H 238 GLN cc_start: 0.8064 (tt0) cc_final: 0.7038 (tm-30) outliers start: 36 outliers final: 29 residues processed: 313 average time/residue: 0.3368 time to fit residues: 160.8581 Evaluate side-chains 302 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 594 GLU 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 103 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 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 79 THR 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 22 CYS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 93 ASP 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 180 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 8 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 ASN ** G 247 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.160240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120191 restraints weight = 26738.315| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.56 r_work: 0.3361 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21023 Z= 0.156 Angle : 0.560 9.544 28601 Z= 0.287 Chirality : 0.041 0.219 3330 Planarity : 0.004 0.068 3483 Dihedral : 13.991 135.349 3205 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.86 % Allowed : 16.41 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2466 helix: 1.73 (0.16), residues: 1140 sheet: -0.36 (0.23), residues: 520 loop : -0.37 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 15 HIS 0.005 0.001 HIS B 108 PHE 0.013 0.001 PHE A 335 TYR 0.028 0.001 TYR B 186 ARG 0.015 0.000 ARG H 61 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1063) hydrogen bonds : angle 4.15303 ( 3040) covalent geometry : bond 0.00370 (21023) covalent geometry : angle 0.55980 (28601) ********************** 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 311 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.7793 (mt) cc_final: 0.7387 (tt) REVERT: A 399 MET cc_start: 0.7236 (ppp) cc_final: 0.5284 (mtt) REVERT: A 445 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7728 (ttp-170) REVERT: A 471 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6756 (tt) REVERT: A 594 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6094 (tp30) REVERT: A 660 MET cc_start: 0.7492 (ttm) cc_final: 0.7244 (ttp) REVERT: C 17 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: C 69 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 119 MET cc_start: 0.5605 (mmm) cc_final: 0.5020 (mmm) REVERT: F 163 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7997 (p) REVERT: G 149 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8254 (mtm110) REVERT: G 188 MSE cc_start: 0.5693 (mpp) cc_final: 0.4995 (mpp) REVERT: G 199 MSE cc_start: 0.6762 (tpp) cc_final: 0.4722 (mmm) REVERT: G 223 ASP cc_start: 0.6480 (p0) cc_final: 0.6100 (p0) REVERT: G 228 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7951 (mtt-85) REVERT: H 14 ARG cc_start: 0.8957 (mtm-85) cc_final: 0.8299 (mtm-85) outliers start: 41 outliers final: 33 residues processed: 301 average time/residue: 0.3447 time to fit residues: 157.6693 Evaluate side-chains 302 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 MET 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 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 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU 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 C residue 316 ASP 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 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 111 ILE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 40 VAL 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 180 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 111 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** 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 = 0.4029 r_free = 0.4029 target = 0.161487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120732 restraints weight = 27419.182| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.64 r_work: 0.3368 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2331 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= 0.137 Angle : 0.558 9.612 28601 Z= 0.286 Chirality : 0.040 0.214 3330 Planarity : 0.004 0.058 3483 Dihedral : 13.996 135.424 3205 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.95 % Allowed : 16.32 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2466 helix: 1.73 (0.16), residues: 1141 sheet: -0.35 (0.23), residues: 521 loop : -0.35 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 15 HIS 0.005 0.001 HIS B 108 PHE 0.024 0.001 PHE A 335 TYR 0.027 0.001 TYR B 186 ARG 0.014 0.000 ARG H 61 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 1063) hydrogen bonds : angle 4.12830 ( 3040) covalent geometry : bond 0.00321 (21023) covalent geometry : angle 0.55789 (28601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10322.15 seconds wall clock time: 177 minutes 54.81 seconds (10674.81 seconds total)