Starting phenix.real_space_refine on Sun Aug 24 15:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.map" model { file = "/net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c82_16469/08_2025/8c82_16469.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 110 5.16 5 C 13534 2.51 5 N 3486 2.21 5 O 3938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "B" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 25, 'TRANS': 479} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "D" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "F" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 479} Chain: "G" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'Z8A': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.83, per 1000 atoms: 0.23 Number of scatterers: 21070 At special positions: 0 Unit cell: (106.26, 175.56, 122.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 2 15.00 O 3938 8.00 N 3486 7.00 C 13534 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 825.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 14 sheets defined 53.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.130A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.515A pdb=" N GLN A 82 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 103 removed outlier: 4.139A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 128 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 179 Proline residue: A 168 - end of helix removed outlier: 4.066A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.035A pdb=" N TRP A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Proline residue: A 203 - end of helix Processing helix chain 'B' and resid 53 through 73 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.801A pdb=" N LYS B 85 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.662A pdb=" N ASP B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 4.888A pdb=" N TRP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.586A pdb=" N GLU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.678A pdb=" N TYR B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.583A pdb=" N THR B 226 " --> pdb=" O PRO B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 239 through 250 removed outlier: 4.218A pdb=" N ARG B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.777A pdb=" N LEU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.831A pdb=" N LEU B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.762A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.193A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.813A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.136A pdb=" N GLN B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.040A pdb=" N SER B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 503 removed outlier: 3.622A pdb=" N GLU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.533A pdb=" N GLN B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 554 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.957A pdb=" N LEU C 37 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 85 removed outlier: 4.059A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 removed outlier: 3.582A pdb=" N ILE C 114 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 5.360A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.562A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 4.321A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 272 through 286 Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.506A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 4.129A pdb=" N ILE C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.588A pdb=" N VAL C 357 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.026A pdb=" N ARG C 384 " --> pdb=" O TRP C 380 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 399 through 414 removed outlier: 3.550A pdb=" N LEU C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 Processing helix chain 'C' and resid 464 through 476 removed outlier: 4.094A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 541 through 553 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.820A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 103 removed outlier: 4.305A pdb=" N VAL E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 128 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 179 Proline residue: E 168 - end of helix removed outlier: 3.807A pdb=" N ALA E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.556A pdb=" N TRP E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'F' and resid 53 through 73 removed outlier: 3.625A pdb=" N VAL F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 4.136A pdb=" N LYS F 85 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 100 Processing helix chain 'F' and resid 110 through 120 removed outlier: 4.885A pdb=" N TRP F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 189 through 204 removed outlier: 3.661A pdb=" N TYR F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 223 through 226 removed outlier: 3.603A pdb=" N THR F 226 " --> pdb=" O PRO F 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 226' Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.157A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 279 removed outlier: 3.865A pdb=" N LEU F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.827A pdb=" N LEU F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 3.764A pdb=" N HIS F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 342 through 347 Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.157A pdb=" N ILE F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 389 through 406 removed outlier: 3.822A pdb=" N VAL F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 427 removed outlier: 4.106A pdb=" N GLN F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 459 Processing helix chain 'F' and resid 461 through 476 Processing helix chain 'F' and resid 482 through 503 removed outlier: 3.635A pdb=" N GLU F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN F 502 " --> pdb=" O HIS F 498 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 503 " --> pdb=" O ALA F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.528A pdb=" N GLN F 516 " --> pdb=" O VAL F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 554 Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.804A pdb=" N LEU G 37 " --> pdb=" O PRO G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 85 removed outlier: 3.962A pdb=" N SER G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 71 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 72 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.731A pdb=" N LEU G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.649A pdb=" N ARG G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 5.395A pdb=" N ASP G 120 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 122 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 Processing helix chain 'G' and resid 200 through 215 removed outlier: 3.553A pdb=" N ILE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 removed outlier: 4.338A pdb=" N PHE G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 250 through 261 Processing helix chain 'G' and resid 272 through 286 Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.630A pdb=" N LEU G 317 " --> pdb=" O ASN G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 removed outlier: 4.128A pdb=" N ILE G 349 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 345 through 350' Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.927A pdb=" N ARG G 384 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 399 through 414 Processing helix chain 'G' and resid 421 through 444 Processing helix chain 'G' and resid 464 through 476 removed outlier: 4.079A pdb=" N ALA G 468 " --> pdb=" O SER G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 523 Processing helix chain 'G' and resid 541 through 553 Proline residue: G 550 - end of helix Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 25 through 45 removed outlier: 3.874A pdb=" N THR H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS H 45 " --> pdb=" O THR H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 removed outlier: 5.966A pdb=" N ILE B 133 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.516A pdb=" N ILE B 349 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 286 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE B 318 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE B 288 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP B 320 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 290 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.898A pdb=" N THR B 508 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.113A pdb=" N ARG C 135 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 479 " --> pdb=" O PRO C 156 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET C 158 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.652A pdb=" N GLY C 362 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 361 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 301 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 246 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU C 302 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.563A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'F' and resid 123 through 124 removed outlier: 5.944A pdb=" N ILE F 133 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 142 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU F 506 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE F 148 " --> pdb=" O LEU F 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 207 through 211 removed outlier: 3.513A pdb=" N ILE F 349 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS F 286 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE F 318 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE F 288 " --> pdb=" O PHE F 318 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP F 320 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR F 290 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 231 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL F 289 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 233 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU F 291 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 434 through 436 removed outlier: 3.923A pdb=" N THR F 508 " --> pdb=" O LYS F 526 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 126 through 127 removed outlier: 4.117A pdb=" N ARG G 135 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA G 153 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ILE G 140 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER G 151 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS G 142 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR G 149 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA G 479 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET G 158 " --> pdb=" O ALA G 479 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY G 362 " --> pdb=" O TYR G 374 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 359 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 361 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE G 297 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE G 329 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE G 299 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP G 331 " --> pdb=" O ILE G 299 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA G 301 " --> pdb=" O ASP G 331 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP G 246 " --> pdb=" O CYS G 300 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU G 302 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 455 through 460 removed outlier: 3.684A pdb=" N ARG G 494 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL G 481 " --> pdb=" O ARG G 496 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5160 1.33 - 1.45: 4111 1.45 - 1.57: 12125 1.57 - 1.69: 2 1.69 - 1.81: 166 Bond restraints: 21564 Sorted by residual: bond pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C4 Z8A E 301 " pdb=" O2 Z8A E 301 " ideal model delta sigma weight residual 1.412 1.355 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" N TYR G 485 " pdb=" CA TYR G 485 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.07e+00 bond pdb=" C3 Z8A E 301 " pdb=" O1 Z8A E 301 " ideal model delta sigma weight residual 1.413 1.365 0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" N TYR C 485 " pdb=" CA TYR C 485 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.91e+00 ... (remaining 21559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 28431 1.56 - 3.13: 646 3.13 - 4.69: 135 4.69 - 6.25: 36 6.25 - 7.82: 18 Bond angle restraints: 29266 Sorted by residual: angle pdb=" C GLN B 84 " pdb=" CA GLN B 84 " pdb=" CB GLN B 84 " ideal model delta sigma weight residual 110.88 104.00 6.88 1.57e+00 4.06e-01 1.92e+01 angle pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" C PHE D 48 " ideal model delta sigma weight residual 114.31 109.01 5.30 1.29e+00 6.01e-01 1.69e+01 angle pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 124.52 -6.08 1.59e+00 3.96e-01 1.46e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" CB PRO B 86 " ideal model delta sigma weight residual 103.25 107.00 -3.75 1.05e+00 9.07e-01 1.28e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" C PRO B 86 " ideal model delta sigma weight residual 112.47 105.39 7.08 2.06e+00 2.36e-01 1.18e+01 ... (remaining 29261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 12714 29.40 - 58.79: 453 58.79 - 88.19: 72 88.19 - 117.59: 36 117.59 - 146.99: 11 Dihedral angle restraints: 13286 sinusoidal: 5630 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta harmonic sigma weight residual -180.00 -53.94 -126.06 0 5.00e+00 4.00e-02 6.36e+02 dihedral pdb=" C4 Z8A E 301 " pdb=" C2 Z8A E 301 " pdb=" C3 Z8A E 301 " pdb=" N1 Z8A E 301 " ideal model delta sinusoidal sigma weight residual 304.92 157.93 146.99 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C16 Z8A E 301 " pdb=" C17 Z8A E 301 " pdb=" C18 Z8A E 301 " pdb=" C6 Z8A E 301 " ideal model delta sinusoidal sigma weight residual 59.65 -154.76 -145.59 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 13283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2969 0.067 - 0.134: 342 0.134 - 0.200: 10 0.200 - 0.267: 3 0.267 - 0.334: 4 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C4 Z8A A 301 " pdb=" C3 Z8A A 301 " pdb=" C5 Z8A A 301 " pdb=" O2 Z8A A 301 " both_signs ideal model delta sigma weight residual False -2.29 -2.62 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C51 Q7G E 302 " pdb=" C41 Q7G E 302 " pdb=" C61 Q7G E 302 " pdb=" O51 Q7G E 302 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C51 Q7G C 602 " pdb=" C41 Q7G C 602 " pdb=" C61 Q7G C 602 " pdb=" O51 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3325 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G E 302 " -0.016 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C13 Q7G E 302 " -0.009 2.00e-02 2.50e+03 pdb=" C14 Q7G E 302 " -0.095 2.00e-02 2.50e+03 pdb=" C15 Q7G E 302 " 0.069 2.00e-02 2.50e+03 pdb=" C16 Q7G E 302 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 212 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 213 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 556 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASP G 556 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP G 556 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS G 557 " -0.010 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 205 2.67 - 3.22: 19041 3.22 - 3.78: 29332 3.78 - 4.34: 38780 4.34 - 4.90: 68830 Nonbonded interactions: 156188 Sorted by model distance: nonbonded pdb=" OD1 ASP C 238 " pdb=" N LYS C 239 " model vdw 2.108 3.120 nonbonded pdb=" OD1 ASP G 238 " pdb=" N LYS G 239 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR F 460 " pdb=" OE1 GLU F 488 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 491 " pdb=" OG SER B 494 " model vdw 2.250 3.040 nonbonded pdb=" O GLN F 77 " pdb=" OG SER F 80 " model vdw 2.280 3.040 ... (remaining 156183 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 'A' selection = (chain 'E' and resid 39 through 301) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 8 through 601) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 0.066 21566 Z= 0.154 Angle : 0.622 7.815 29266 Z= 0.329 Chirality : 0.044 0.334 3328 Planarity : 0.004 0.058 3688 Dihedral : 17.017 146.987 8354 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 2602 helix: 2.30 (0.16), residues: 1152 sheet: 0.69 (0.32), residues: 234 loop : -1.19 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 456 TYR 0.018 0.001 TYR G 510 PHE 0.030 0.001 PHE E 163 TRP 0.016 0.001 TRP E 112 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00308 (21564) covalent geometry : angle 0.62216 (29266) hydrogen bonds : bond 0.17543 ( 984) hydrogen bonds : angle 5.81300 ( 2829) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 86 TRP cc_start: 0.7150 (m-10) cc_final: 0.4899 (m-90) REVERT: A 163 PHE cc_start: 0.8676 (t80) cc_final: 0.8151 (t80) REVERT: A 209 ARG cc_start: 0.6282 (mmt-90) cc_final: 0.5941 (mmt-90) REVERT: A 220 GLN cc_start: 0.8094 (mt0) cc_final: 0.7841 (mt0) REVERT: B 265 GLU cc_start: 0.6925 (tt0) cc_final: 0.6705 (tt0) REVERT: B 274 GLN cc_start: 0.8238 (tp40) cc_final: 0.7957 (tm-30) REVERT: C 409 SER cc_start: 0.8404 (m) cc_final: 0.8108 (m) REVERT: C 534 ASP cc_start: 0.8245 (m-30) cc_final: 0.7626 (p0) REVERT: D 7 SER cc_start: 0.8826 (t) cc_final: 0.8590 (p) REVERT: E 174 VAL cc_start: 0.8418 (t) cc_final: 0.7986 (p) REVERT: E 209 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.5949 (mpt180) REVERT: F 99 ASP cc_start: 0.8604 (t0) cc_final: 0.8142 (t0) REVERT: F 274 GLN cc_start: 0.8202 (tp40) cc_final: 0.7920 (tm-30) REVERT: G 97 ASP cc_start: 0.7805 (t0) cc_final: 0.7228 (t70) REVERT: G 409 SER cc_start: 0.8671 (t) cc_final: 0.8458 (t) REVERT: G 548 ARG cc_start: 0.7367 (tpp80) cc_final: 0.6691 (mtp180) REVERT: H 5 LYS cc_start: 0.7966 (tppt) cc_final: 0.7703 (tttm) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.1464 time to fit residues: 76.3249 Evaluate side-chains 218 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS E 189 ASN F 237 GLN G 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144299 restraints weight = 26623.837| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.49 r_work: 0.3634 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21566 Z= 0.186 Angle : 0.631 8.689 29266 Z= 0.325 Chirality : 0.046 0.238 3328 Planarity : 0.005 0.054 3688 Dihedral : 12.045 148.160 3346 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.30 % Allowed : 6.48 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2602 helix: 2.31 (0.15), residues: 1180 sheet: 0.18 (0.34), residues: 212 loop : -1.25 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.026 0.002 TYR C 510 PHE 0.023 0.002 PHE B 364 TRP 0.009 0.001 TRP C 540 HIS 0.007 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00460 (21564) covalent geometry : angle 0.63075 (29266) hydrogen bonds : bond 0.05991 ( 984) hydrogen bonds : angle 4.47471 ( 2829) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.907 Fit side-chains REVERT: A 86 TRP cc_start: 0.7322 (m-10) cc_final: 0.4789 (m-90) REVERT: A 163 PHE cc_start: 0.8514 (t80) cc_final: 0.8268 (t80) REVERT: A 209 ARG cc_start: 0.6340 (mmt-90) cc_final: 0.5939 (mmt-90) REVERT: B 99 ASP cc_start: 0.8638 (t0) cc_final: 0.8304 (t0) REVERT: B 274 GLN cc_start: 0.8228 (tp40) cc_final: 0.7610 (tm-30) REVERT: C 409 SER cc_start: 0.8507 (m) cc_final: 0.8241 (m) REVERT: C 534 ASP cc_start: 0.8857 (m-30) cc_final: 0.7840 (p0) REVERT: D 7 SER cc_start: 0.8986 (t) cc_final: 0.8580 (p) REVERT: E 174 VAL cc_start: 0.8067 (t) cc_final: 0.7724 (p) REVERT: E 177 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7347 (t-90) REVERT: E 209 ARG cc_start: 0.6513 (mmt-90) cc_final: 0.6136 (mpt180) REVERT: F 99 ASP cc_start: 0.8638 (t0) cc_final: 0.8238 (t0) REVERT: F 265 GLU cc_start: 0.7689 (tt0) cc_final: 0.7376 (tt0) REVERT: F 274 GLN cc_start: 0.8254 (tp40) cc_final: 0.7668 (tm-30) REVERT: F 463 GLU cc_start: 0.7635 (mp0) cc_final: 0.7342 (mp0) REVERT: G 97 ASP cc_start: 0.8212 (t0) cc_final: 0.7586 (t70) REVERT: G 115 LYS cc_start: 0.8237 (tptm) cc_final: 0.7947 (tttt) REVERT: G 116 MET cc_start: 0.8251 (tpp) cc_final: 0.7948 (tpp) REVERT: G 218 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: G 409 SER cc_start: 0.8885 (t) cc_final: 0.8674 (t) REVERT: G 548 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7147 (ttm170) REVERT: G 556 ASP cc_start: 0.7961 (t70) cc_final: 0.7391 (t70) REVERT: H 5 LYS cc_start: 0.8019 (tppt) cc_final: 0.7579 (tttm) outliers start: 30 outliers final: 21 residues processed: 238 average time/residue: 0.1649 time to fit residues: 60.3208 Evaluate side-chains 227 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 25 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 181 optimal weight: 0.0770 chunk 143 optimal weight: 10.0000 chunk 115 optimal weight: 0.0070 chunk 5 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 172 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151656 restraints weight = 26654.300| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.52 r_work: 0.3731 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21566 Z= 0.095 Angle : 0.506 7.752 29266 Z= 0.252 Chirality : 0.042 0.368 3328 Planarity : 0.004 0.082 3688 Dihedral : 9.593 145.455 3346 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 1.04 % Allowed : 8.64 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.17), residues: 2602 helix: 2.57 (0.15), residues: 1172 sheet: 0.57 (0.32), residues: 266 loop : -1.13 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 212 TYR 0.017 0.001 TYR F 71 PHE 0.021 0.001 PHE E 172 TRP 0.007 0.001 TRP G 294 HIS 0.002 0.000 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00196 (21564) covalent geometry : angle 0.50571 (29266) hydrogen bonds : bond 0.03756 ( 984) hydrogen bonds : angle 4.07761 ( 2829) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.822 Fit side-chains REVERT: A 86 TRP cc_start: 0.7264 (m-10) cc_final: 0.4794 (m-90) REVERT: A 163 PHE cc_start: 0.8461 (t80) cc_final: 0.7930 (t80) REVERT: A 209 ARG cc_start: 0.6166 (mmt-90) cc_final: 0.5729 (mpt180) REVERT: B 114 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: B 274 GLN cc_start: 0.8171 (tp40) cc_final: 0.7536 (mt0) REVERT: C 107 GLU cc_start: 0.7818 (pm20) cc_final: 0.7572 (pm20) REVERT: C 145 ASN cc_start: 0.8104 (m-40) cc_final: 0.7871 (m-40) REVERT: C 409 SER cc_start: 0.8380 (m) cc_final: 0.8139 (m) REVERT: C 534 ASP cc_start: 0.8840 (m-30) cc_final: 0.7806 (p0) REVERT: D 7 SER cc_start: 0.9013 (t) cc_final: 0.8549 (p) REVERT: D 51 MET cc_start: 0.8396 (mmm) cc_final: 0.8134 (mmm) REVERT: E 174 VAL cc_start: 0.8067 (t) cc_final: 0.7775 (p) REVERT: E 177 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: E 209 ARG cc_start: 0.6332 (mmt-90) cc_final: 0.6003 (mpt180) REVERT: F 99 ASP cc_start: 0.8640 (t0) cc_final: 0.8260 (t0) REVERT: F 114 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: F 274 GLN cc_start: 0.8182 (tp40) cc_final: 0.7557 (tm-30) REVERT: F 424 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7632 (t80) REVERT: F 463 GLU cc_start: 0.7563 (mp0) cc_final: 0.7255 (mp0) REVERT: G 97 ASP cc_start: 0.8228 (t0) cc_final: 0.7604 (t70) REVERT: G 116 MET cc_start: 0.8089 (tpp) cc_final: 0.7861 (tpp) REVERT: G 212 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7418 (ttp-170) REVERT: G 272 MET cc_start: 0.6801 (mmt) cc_final: 0.6356 (mmt) REVERT: G 548 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7064 (mtp180) REVERT: G 552 ASP cc_start: 0.8734 (m-30) cc_final: 0.8446 (m-30) outliers start: 24 outliers final: 12 residues processed: 237 average time/residue: 0.1475 time to fit residues: 54.0624 Evaluate side-chains 214 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 144 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 76 ASN A 220 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147065 restraints weight = 26747.040| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.49 r_work: 0.3674 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21566 Z= 0.123 Angle : 0.529 11.926 29266 Z= 0.267 Chirality : 0.043 0.398 3328 Planarity : 0.004 0.093 3688 Dihedral : 9.314 141.831 3346 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 1.60 % Allowed : 9.64 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.17), residues: 2602 helix: 2.60 (0.15), residues: 1174 sheet: 0.78 (0.33), residues: 240 loop : -1.11 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.018 0.001 TYR G 510 PHE 0.015 0.001 PHE B 318 TRP 0.011 0.001 TRP C 540 HIS 0.003 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00292 (21564) covalent geometry : angle 0.52904 (29266) hydrogen bonds : bond 0.04491 ( 984) hydrogen bonds : angle 4.00828 ( 2829) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.860 Fit side-chains REVERT: A 86 TRP cc_start: 0.7307 (m-10) cc_final: 0.4703 (m-90) REVERT: A 163 PHE cc_start: 0.8487 (t80) cc_final: 0.8240 (t80) REVERT: A 209 ARG cc_start: 0.6144 (mmt-90) cc_final: 0.5835 (mpt180) REVERT: B 114 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 274 GLN cc_start: 0.8137 (tp40) cc_final: 0.7498 (mt0) REVERT: B 279 LYS cc_start: 0.5952 (pttt) cc_final: 0.5337 (ttmt) REVERT: C 145 ASN cc_start: 0.8107 (m-40) cc_final: 0.7693 (m-40) REVERT: C 409 SER cc_start: 0.8405 (m) cc_final: 0.8149 (m) REVERT: D 7 SER cc_start: 0.8964 (t) cc_final: 0.8513 (p) REVERT: E 174 VAL cc_start: 0.8046 (t) cc_final: 0.7758 (p) REVERT: E 209 ARG cc_start: 0.6318 (mmt-90) cc_final: 0.6008 (mpt180) REVERT: F 99 ASP cc_start: 0.8663 (t0) cc_final: 0.8309 (t0) REVERT: F 114 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: F 274 GLN cc_start: 0.8180 (tp40) cc_final: 0.7555 (tm-30) REVERT: F 424 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7826 (t80) REVERT: F 463 GLU cc_start: 0.7605 (mp0) cc_final: 0.7264 (mp0) REVERT: G 97 ASP cc_start: 0.8257 (t0) cc_final: 0.7662 (t70) REVERT: G 116 MET cc_start: 0.8104 (tpp) cc_final: 0.7893 (tpp) REVERT: G 272 MET cc_start: 0.7033 (mmt) cc_final: 0.6555 (mmt) REVERT: G 548 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7151 (mtp180) REVERT: H 8 MET cc_start: 0.8431 (ttt) cc_final: 0.8086 (ttt) outliers start: 37 outliers final: 24 residues processed: 233 average time/residue: 0.1436 time to fit residues: 52.4432 Evaluate side-chains 218 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.186943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140262 restraints weight = 26960.041| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.51 r_work: 0.3597 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 21566 Z= 0.232 Angle : 0.651 11.351 29266 Z= 0.336 Chirality : 0.047 0.367 3328 Planarity : 0.005 0.094 3688 Dihedral : 9.268 137.272 3346 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 10.29 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2602 helix: 2.45 (0.15), residues: 1158 sheet: -0.00 (0.34), residues: 216 loop : -1.40 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.027 0.002 TYR G 510 PHE 0.026 0.002 PHE B 318 TRP 0.015 0.001 TRP C 540 HIS 0.005 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00594 (21564) covalent geometry : angle 0.65130 (29266) hydrogen bonds : bond 0.06640 ( 984) hydrogen bonds : angle 4.24764 ( 2829) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.753 Fit side-chains REVERT: A 209 ARG cc_start: 0.6380 (mmt-90) cc_final: 0.6156 (mpt180) REVERT: B 99 ASP cc_start: 0.8633 (t0) cc_final: 0.8275 (t0) REVERT: B 114 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: B 274 GLN cc_start: 0.8213 (tp40) cc_final: 0.7593 (tm-30) REVERT: B 279 LYS cc_start: 0.6292 (pttt) cc_final: 0.5645 (ttmt) REVERT: B 377 ILE cc_start: 0.8577 (tp) cc_final: 0.8167 (mt) REVERT: B 463 GLU cc_start: 0.7777 (mp0) cc_final: 0.7367 (mp0) REVERT: C 409 SER cc_start: 0.8500 (m) cc_final: 0.8255 (m) REVERT: D 7 SER cc_start: 0.8946 (t) cc_final: 0.8478 (p) REVERT: E 174 VAL cc_start: 0.8152 (t) cc_final: 0.7873 (p) REVERT: E 209 ARG cc_start: 0.6500 (mmt-90) cc_final: 0.6231 (mpt180) REVERT: F 99 ASP cc_start: 0.8719 (t0) cc_final: 0.8341 (t0) REVERT: F 114 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: F 274 GLN cc_start: 0.8228 (tp40) cc_final: 0.7612 (tm-30) REVERT: F 279 LYS cc_start: 0.6354 (pttt) cc_final: 0.5747 (ttmt) REVERT: F 463 GLU cc_start: 0.7721 (mp0) cc_final: 0.7330 (mp0) REVERT: G 97 ASP cc_start: 0.8341 (t0) cc_final: 0.7776 (t70) REVERT: G 116 MET cc_start: 0.8271 (tpp) cc_final: 0.8029 (tpp) REVERT: G 218 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: G 272 MET cc_start: 0.7314 (mmt) cc_final: 0.6803 (mmt) REVERT: G 548 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7190 (mtp180) REVERT: H 8 MET cc_start: 0.8559 (ttt) cc_final: 0.8200 (ttt) outliers start: 49 outliers final: 34 residues processed: 234 average time/residue: 0.1349 time to fit residues: 49.3438 Evaluate side-chains 223 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 194 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 242 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146076 restraints weight = 26631.369| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.51 r_work: 0.3577 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21566 Z= 0.116 Angle : 0.532 12.100 29266 Z= 0.267 Chirality : 0.043 0.356 3328 Planarity : 0.004 0.093 3688 Dihedral : 8.879 138.309 3346 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.99 % Allowed : 11.06 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2602 helix: 2.53 (0.15), residues: 1170 sheet: 0.53 (0.33), residues: 264 loop : -1.22 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.018 0.001 TYR F 71 PHE 0.016 0.001 PHE A 163 TRP 0.016 0.001 TRP A 86 HIS 0.003 0.001 HIS F 421 Details of bonding type rmsd covalent geometry : bond 0.00270 (21564) covalent geometry : angle 0.53239 (29266) hydrogen bonds : bond 0.04331 ( 984) hydrogen bonds : angle 3.98799 ( 2829) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.707 Fit side-chains REVERT: A 209 ARG cc_start: 0.6342 (mmt-90) cc_final: 0.6082 (mpt180) REVERT: B 114 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: B 274 GLN cc_start: 0.8183 (tp40) cc_final: 0.7551 (mt0) REVERT: B 377 ILE cc_start: 0.8491 (tp) cc_final: 0.8180 (mt) REVERT: C 107 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: C 218 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: D 7 SER cc_start: 0.8919 (t) cc_final: 0.8438 (p) REVERT: E 174 VAL cc_start: 0.8104 (t) cc_final: 0.7818 (p) REVERT: E 209 ARG cc_start: 0.6523 (mmt-90) cc_final: 0.6238 (mpt180) REVERT: F 99 ASP cc_start: 0.8627 (t0) cc_final: 0.8266 (t0) REVERT: F 114 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: F 274 GLN cc_start: 0.8225 (tp40) cc_final: 0.7592 (tm-30) REVERT: F 279 LYS cc_start: 0.5967 (pttt) cc_final: 0.5371 (ttmt) REVERT: F 463 GLU cc_start: 0.7640 (mp0) cc_final: 0.7307 (mp0) REVERT: G 97 ASP cc_start: 0.8303 (t0) cc_final: 0.7681 (t70) REVERT: G 116 MET cc_start: 0.8208 (tpp) cc_final: 0.7967 (tpp) REVERT: G 272 MET cc_start: 0.7006 (mmt) cc_final: 0.6644 (mmt) REVERT: G 548 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7097 (mtp180) REVERT: H 8 MET cc_start: 0.8395 (ttt) cc_final: 0.7994 (ttt) outliers start: 46 outliers final: 30 residues processed: 232 average time/residue: 0.1476 time to fit residues: 53.8440 Evaluate side-chains 217 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 5 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 0.0050 chunk 147 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 76 ASN ** 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 = 0.4203 r_free = 0.4203 target = 0.188420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141717 restraints weight = 26964.924| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.54 r_work: 0.3397 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21566 Z= 0.176 Angle : 0.589 9.529 29266 Z= 0.302 Chirality : 0.045 0.491 3328 Planarity : 0.005 0.091 3688 Dihedral : 8.821 134.126 3346 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.16 % Allowed : 11.97 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.17), residues: 2602 helix: 2.53 (0.15), residues: 1160 sheet: 0.46 (0.34), residues: 240 loop : -1.41 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.022 0.002 TYR G 510 PHE 0.029 0.002 PHE E 191 TRP 0.017 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00440 (21564) covalent geometry : angle 0.58923 (29266) hydrogen bonds : bond 0.05667 ( 984) hydrogen bonds : angle 4.08979 ( 2829) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.732 Fit side-chains REVERT: A 209 ARG cc_start: 0.6290 (mmt-90) cc_final: 0.6078 (mpt180) REVERT: B 114 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: B 274 GLN cc_start: 0.8224 (tp40) cc_final: 0.7613 (mt0) REVERT: B 279 LYS cc_start: 0.6016 (pttt) cc_final: 0.5419 (ttmt) REVERT: B 377 ILE cc_start: 0.8524 (tp) cc_final: 0.8124 (mt) REVERT: C 107 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: D 7 SER cc_start: 0.8914 (t) cc_final: 0.8420 (p) REVERT: E 174 VAL cc_start: 0.8129 (t) cc_final: 0.7845 (p) REVERT: E 209 ARG cc_start: 0.6512 (mmt-90) cc_final: 0.6240 (mpt180) REVERT: F 99 ASP cc_start: 0.8649 (t0) cc_final: 0.8269 (t0) REVERT: F 114 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: F 274 GLN cc_start: 0.8252 (tp40) cc_final: 0.7661 (tm-30) REVERT: F 279 LYS cc_start: 0.6145 (pttt) cc_final: 0.5556 (ttmt) REVERT: F 463 GLU cc_start: 0.7697 (mp0) cc_final: 0.7310 (mp0) REVERT: G 97 ASP cc_start: 0.8155 (t0) cc_final: 0.7552 (t70) REVERT: G 116 MET cc_start: 0.8086 (tpp) cc_final: 0.7833 (tpp) REVERT: G 272 MET cc_start: 0.7167 (mmt) cc_final: 0.6713 (mmt) REVERT: G 548 ARG cc_start: 0.7818 (tpp80) cc_final: 0.7049 (mtp180) REVERT: H 8 MET cc_start: 0.8392 (ttt) cc_final: 0.8025 (ttt) outliers start: 50 outliers final: 40 residues processed: 230 average time/residue: 0.1450 time to fit residues: 52.0873 Evaluate side-chains 223 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 242 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 168 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 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 = 0.4234 r_free = 0.4234 target = 0.192251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145457 restraints weight = 26663.249| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.55 r_work: 0.3665 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21566 Z= 0.115 Angle : 0.525 8.770 29266 Z= 0.266 Chirality : 0.043 0.461 3328 Planarity : 0.004 0.089 3688 Dihedral : 8.535 133.810 3346 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.99 % Allowed : 12.40 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.17), residues: 2602 helix: 2.56 (0.15), residues: 1170 sheet: 0.70 (0.32), residues: 274 loop : -1.27 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.018 0.001 TYR F 71 PHE 0.023 0.001 PHE E 191 TRP 0.014 0.001 TRP C 540 HIS 0.002 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00271 (21564) covalent geometry : angle 0.52531 (29266) hydrogen bonds : bond 0.04325 ( 984) hydrogen bonds : angle 3.95256 ( 2829) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.905 Fit side-chains REVERT: A 209 ARG cc_start: 0.6350 (mmt-90) cc_final: 0.6124 (mpt180) REVERT: B 114 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: B 274 GLN cc_start: 0.8195 (tp40) cc_final: 0.7566 (mt0) REVERT: B 377 ILE cc_start: 0.8470 (tp) cc_final: 0.8106 (mt) REVERT: C 97 ASP cc_start: 0.8456 (t0) cc_final: 0.7893 (p0) REVERT: C 107 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: D 7 SER cc_start: 0.8925 (t) cc_final: 0.8399 (p) REVERT: E 163 PHE cc_start: 0.8382 (t80) cc_final: 0.8068 (t80) REVERT: E 174 VAL cc_start: 0.8064 (t) cc_final: 0.7783 (p) REVERT: E 209 ARG cc_start: 0.6567 (mmt-90) cc_final: 0.6293 (mpt180) REVERT: F 99 ASP cc_start: 0.8650 (t0) cc_final: 0.8276 (t0) REVERT: F 114 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: F 274 GLN cc_start: 0.8203 (tp40) cc_final: 0.7557 (tm-30) REVERT: F 279 LYS cc_start: 0.5915 (pttt) cc_final: 0.5357 (ttmt) REVERT: G 97 ASP cc_start: 0.8307 (t0) cc_final: 0.7701 (t70) REVERT: G 116 MET cc_start: 0.8181 (tpp) cc_final: 0.7953 (tpp) REVERT: G 272 MET cc_start: 0.7037 (mmt) cc_final: 0.6648 (mmt) REVERT: G 548 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7039 (mtp180) REVERT: H 8 MET cc_start: 0.8380 (ttt) cc_final: 0.8053 (ttt) outliers start: 46 outliers final: 37 residues processed: 223 average time/residue: 0.1569 time to fit residues: 54.1063 Evaluate side-chains 220 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 291 ASN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148642 restraints weight = 26665.808| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.49 r_work: 0.3713 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21566 Z= 0.094 Angle : 0.496 8.118 29266 Z= 0.249 Chirality : 0.042 0.433 3328 Planarity : 0.004 0.086 3688 Dihedral : 8.123 129.275 3346 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.64 % Allowed : 12.71 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.17), residues: 2602 helix: 2.67 (0.15), residues: 1172 sheet: 0.74 (0.32), residues: 278 loop : -1.11 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.018 0.001 TYR F 71 PHE 0.027 0.001 PHE E 172 TRP 0.009 0.001 TRP G 294 HIS 0.002 0.000 HIS G 514 Details of bonding type rmsd covalent geometry : bond 0.00207 (21564) covalent geometry : angle 0.49634 (29266) hydrogen bonds : bond 0.03454 ( 984) hydrogen bonds : angle 3.80812 ( 2829) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.026 Fit side-chains REVERT: A 209 ARG cc_start: 0.6320 (mmt-90) cc_final: 0.6089 (mpt180) REVERT: B 274 GLN cc_start: 0.8181 (tp40) cc_final: 0.7543 (mt0) REVERT: B 377 ILE cc_start: 0.8391 (tp) cc_final: 0.8123 (mt) REVERT: C 97 ASP cc_start: 0.8452 (t0) cc_final: 0.7975 (p0) REVERT: C 107 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: D 7 SER cc_start: 0.8905 (t) cc_final: 0.8381 (p) REVERT: E 163 PHE cc_start: 0.8351 (t80) cc_final: 0.8040 (t80) REVERT: E 174 VAL cc_start: 0.8073 (t) cc_final: 0.7820 (p) REVERT: E 209 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6281 (mpt180) REVERT: F 99 ASP cc_start: 0.8668 (t0) cc_final: 0.8325 (t0) REVERT: F 114 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: F 274 GLN cc_start: 0.8172 (tp40) cc_final: 0.7450 (tp40) REVERT: G 97 ASP cc_start: 0.8271 (t0) cc_final: 0.7667 (t70) REVERT: G 272 MET cc_start: 0.6925 (mmt) cc_final: 0.6549 (mmt) REVERT: G 548 ARG cc_start: 0.7754 (tpp80) cc_final: 0.6943 (mtp180) REVERT: H 8 MET cc_start: 0.8239 (ttt) cc_final: 0.7933 (ttt) outliers start: 38 outliers final: 27 residues processed: 221 average time/residue: 0.1433 time to fit residues: 49.9404 Evaluate side-chains 210 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 199 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 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 = 0.4216 r_free = 0.4216 target = 0.189617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142849 restraints weight = 26776.978| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.52 r_work: 0.3546 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21566 Z= 0.162 Angle : 0.570 8.019 29266 Z= 0.293 Chirality : 0.045 0.469 3328 Planarity : 0.004 0.085 3688 Dihedral : 8.194 125.738 3346 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.56 % Allowed : 13.01 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.17), residues: 2602 helix: 2.54 (0.15), residues: 1184 sheet: 0.59 (0.34), residues: 244 loop : -1.18 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.022 0.002 TYR C 510 PHE 0.024 0.002 PHE E 172 TRP 0.013 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00403 (21564) covalent geometry : angle 0.57008 (29266) hydrogen bonds : bond 0.05187 ( 984) hydrogen bonds : angle 3.96688 ( 2829) Misc. bond : bond 0.00006 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.774 Fit side-chains REVERT: B 274 GLN cc_start: 0.8216 (tp40) cc_final: 0.7574 (mt0) REVERT: B 377 ILE cc_start: 0.8508 (tp) cc_final: 0.8197 (mt) REVERT: B 427 ASP cc_start: 0.7265 (m-30) cc_final: 0.6925 (t70) REVERT: C 97 ASP cc_start: 0.8500 (t0) cc_final: 0.7969 (p0) REVERT: C 107 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: D 7 SER cc_start: 0.8903 (t) cc_final: 0.8392 (p) REVERT: E 174 VAL cc_start: 0.8111 (t) cc_final: 0.7852 (p) REVERT: E 209 ARG cc_start: 0.6637 (mmt-90) cc_final: 0.6382 (mpt180) REVERT: F 99 ASP cc_start: 0.8711 (t0) cc_final: 0.8358 (t0) REVERT: F 114 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: F 274 GLN cc_start: 0.8241 (tp40) cc_final: 0.7596 (tm-30) REVERT: F 279 LYS cc_start: 0.5912 (pttt) cc_final: 0.5375 (ttmt) REVERT: G 97 ASP cc_start: 0.8291 (t0) cc_final: 0.7700 (t70) REVERT: G 272 MET cc_start: 0.7150 (mmt) cc_final: 0.6699 (mmt) REVERT: G 548 ARG cc_start: 0.7807 (tpp80) cc_final: 0.6983 (mtp180) REVERT: H 8 MET cc_start: 0.8345 (ttt) cc_final: 0.8018 (ttt) outliers start: 36 outliers final: 33 residues processed: 212 average time/residue: 0.1431 time to fit residues: 47.3291 Evaluate side-chains 212 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 137 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 184 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.192131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141329 restraints weight = 26753.487| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.22 r_work: 0.3474 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21566 Z= 0.123 Angle : 0.536 7.446 29266 Z= 0.273 Chirality : 0.044 0.459 3328 Planarity : 0.004 0.084 3688 Dihedral : 8.058 124.882 3346 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.60 % Allowed : 13.40 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2602 helix: 2.57 (0.15), residues: 1182 sheet: 0.72 (0.32), residues: 274 loop : -1.16 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.018 0.001 TYR F 71 PHE 0.025 0.001 PHE E 172 TRP 0.023 0.001 TRP E 86 HIS 0.003 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00294 (21564) covalent geometry : angle 0.53562 (29266) hydrogen bonds : bond 0.04398 ( 984) hydrogen bonds : angle 3.90600 ( 2829) Misc. bond : bond 0.00005 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.01 seconds wall clock time: 87 minutes 39.69 seconds (5259.69 seconds total)