Starting phenix.real_space_refine on Tue May 27 13:14:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3p_39750/05_2025/8z3p_39750_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3p_39750/05_2025/8z3p_39750.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/8z3p_39750/05_2025/8z3p_39750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3p_39750/05_2025/8z3p_39750.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3p_39750/05_2025/8z3p_39750_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3p_39750/05_2025/8z3p_39750_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 36 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 18494 2.51 5 N 5487 2.21 5 O 5337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29494 Number of models: 1 Model: "" Number of chains: 15 Chain: "X" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "Y" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "Z" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "A" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "B" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "C" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "D" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "E" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "F" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4804 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 39, 'TRANS': 572} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.28, per 1000 atoms: 0.62 Number of scatterers: 29494 At special positions: 0 Unit cell: (97.86, 213.428, 212.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 132 16.00 P 36 15.00 Mg 2 11.99 O 5337 8.00 N 5487 7.00 C 18494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 266 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 264 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 471 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 266 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 264 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 266 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 471 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 264 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 471 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 266 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 264 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 471 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 264 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 266 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 264 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 471 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 266 " 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6812 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 15 sheets defined 52.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 4.062A pdb=" N LEU A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.712A pdb=" N SER A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.584A pdb=" N ALA A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.784A pdb=" N ILE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 199 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.547A pdb=" N GLU A 223 " --> pdb=" O MET A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.782A pdb=" N ARG A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 328 through 346 removed outlier: 3.511A pdb=" N GLN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.733A pdb=" N ALA A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 410 through 428 Processing helix chain 'A' and resid 446 through 453 removed outlier: 3.548A pdb=" N THR A 449 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA A 451 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS A 452 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 453 " --> pdb=" O ARG A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 453' Processing helix chain 'A' and resid 454 through 465 removed outlier: 5.299A pdb=" N ALA A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 4.157A pdb=" N ILE A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.503A pdb=" N LEU A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 500 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.841A pdb=" N CYS A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 42 through 53 removed outlier: 3.536A pdb=" N ARG B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 4.392A pdb=" N HIS B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.627A pdb=" N GLN B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 198 through 217 removed outlier: 4.143A pdb=" N THR B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 242 removed outlier: 3.782A pdb=" N GLU B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.683A pdb=" N ARG B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.892A pdb=" N GLY B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.716A pdb=" N ALA B 361 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.915A pdb=" N GLY B 390 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 391 " --> pdb=" O PRO B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 391' Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 450 through 453 removed outlier: 3.920A pdb=" N TYR B 453 " --> pdb=" O ARG B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 453' Processing helix chain 'B' and resid 454 through 464 removed outlier: 5.216A pdb=" N ALA B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 removed outlier: 4.121A pdb=" N ILE B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 removed outlier: 3.582A pdb=" N GLN B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 553 through 561 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 589 Processing helix chain 'B' and resid 593 through 608 Processing helix chain 'B' and resid 611 through 624 Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.673A pdb=" N GLU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.541A pdb=" N ARG C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 89 removed outlier: 3.808A pdb=" N SER C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 144 through 154 removed outlier: 3.756A pdb=" N ILE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 217 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.618A pdb=" N GLU C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.940A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 310 through 318 removed outlier: 4.115A pdb=" N GLY C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 347 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.745A pdb=" N ALA C 361 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.938A pdb=" N GLY C 390 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 391 " --> pdb=" O PRO C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 446 through 453 removed outlier: 3.563A pdb=" N THR C 449 " --> pdb=" O ASP C 446 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ALA C 451 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS C 452 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 453 " --> pdb=" O ARG C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 453' Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.588A pdb=" N PHE C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.856A pdb=" N ILE C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.599A pdb=" N LEU C 499 " --> pdb=" O ALA C 496 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 553 through 561 Processing helix chain 'C' and resid 570 through 575 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'C' and resid 611 through 625 Processing helix chain 'D' and resid 16 through 23 removed outlier: 3.563A pdb=" N GLU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.587A pdb=" N SER D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.501A pdb=" N ALA D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.736A pdb=" N ARG D 172 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 217 Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 232 through 242 removed outlier: 3.783A pdb=" N GLU D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 274 through 282 removed outlier: 4.104A pdb=" N ARG D 278 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 311 through 317 Processing helix chain 'D' and resid 322 through 327 removed outlier: 3.844A pdb=" N ARG D 327 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 347 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.984A pdb=" N ALA D 361 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.809A pdb=" N GLY D 390 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 391 " --> pdb=" O PRO D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 446 through 453 removed outlier: 3.903A pdb=" N ARG D 450 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA D 451 " --> pdb=" O LYS D 448 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS D 452 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 453 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 removed outlier: 4.610A pdb=" N ALA D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 488 removed outlier: 3.937A pdb=" N ILE D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 removed outlier: 3.542A pdb=" N LEU D 499 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY D 500 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 501' Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 553 through 561 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 577 through 589 removed outlier: 3.531A pdb=" N CYS D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 608 Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.972A pdb=" N LEU E 23 " --> pdb=" O PRO E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 71 through 88 removed outlier: 3.838A pdb=" N HIS E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 198 through 217 Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.690A pdb=" N THR E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 Processing helix chain 'E' and resid 248 through 258 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 273 through 282 removed outlier: 3.607A pdb=" N LEU E 277 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 328 through 346 Processing helix chain 'E' and resid 356 through 361 removed outlier: 3.938A pdb=" N ALA E 361 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 384 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.642A pdb=" N GLY E 390 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 391 " --> pdb=" O PRO E 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 387 through 391' Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 446 through 453 removed outlier: 4.277A pdb=" N ARG E 450 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA E 451 " --> pdb=" O LYS E 448 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS E 452 " --> pdb=" O THR E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 465 removed outlier: 4.414A pdb=" N ALA E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 removed outlier: 4.084A pdb=" N ILE E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 removed outlier: 3.746A pdb=" N LEU E 499 " --> pdb=" O ALA E 496 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY E 500 " --> pdb=" O LEU E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 519 through 527 Processing helix chain 'E' and resid 553 through 561 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 577 through 589 Processing helix chain 'E' and resid 593 through 608 Processing helix chain 'E' and resid 611 through 624 Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.865A pdb=" N GLU F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 53 removed outlier: 3.783A pdb=" N ARG F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 89 removed outlier: 3.900A pdb=" N SER F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 144 through 155 Processing helix chain 'F' and resid 198 through 217 Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 248 through 258 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 274 through 282 removed outlier: 4.014A pdb=" N ARG F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 removed outlier: 3.690A pdb=" N LEU F 290 " --> pdb=" O PRO F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 removed outlier: 4.071A pdb=" N GLY F 318 " --> pdb=" O TYR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 346 removed outlier: 3.658A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 361 removed outlier: 3.860A pdb=" N ALA F 361 " --> pdb=" O ALA F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 384 Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.795A pdb=" N GLY F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 391 " --> pdb=" O PRO F 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 387 through 391' Processing helix chain 'F' and resid 410 through 428 Processing helix chain 'F' and resid 446 through 453 removed outlier: 4.152A pdb=" N ARG F 450 " --> pdb=" O GLU F 447 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA F 451 " --> pdb=" O LYS F 448 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS F 452 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 453 " --> pdb=" O ARG F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 464 removed outlier: 5.019A pdb=" N ALA F 460 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 487 removed outlier: 3.925A pdb=" N ILE F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 501 removed outlier: 3.512A pdb=" N GLN F 501 " --> pdb=" O SER F 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 498 through 501' Processing helix chain 'F' and resid 502 through 513 Processing helix chain 'F' and resid 519 through 527 Processing helix chain 'F' and resid 553 through 561 Processing helix chain 'F' and resid 570 through 575 Processing helix chain 'F' and resid 577 through 589 removed outlier: 3.693A pdb=" N CYS F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 608 Processing helix chain 'F' and resid 611 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 165 removed outlier: 6.150A pdb=" N VAL A 123 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 121 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 96 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS A 6 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS A 99 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 8 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 7 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU A 35 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 9 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 191 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 185 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN A 194 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 183 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 266 removed outlier: 6.014A pdb=" N LYS A 260 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR A 350 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A 264 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG A 354 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS A 266 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 355 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N VAL A 396 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N GLY A 438 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 398 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASP A 440 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 400 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA A 442 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA A 402 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 437 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR A 469 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 439 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS A 471 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 441 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 468 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY A 494 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 470 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU A 493 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 516 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 163 removed outlier: 5.306A pdb=" N ARG B 161 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N HIS B 125 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS B 6 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N CYS B 99 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 8 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU B 186 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 192 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 260 through 261 removed outlier: 7.502A pdb=" N LYS B 260 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 351 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 395 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B 437 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 398 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 439 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU B 400 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 441 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 266 removed outlier: 6.942A pdb=" N CYS B 265 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 395 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B 437 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 398 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 439 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU B 400 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 441 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 437 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR B 469 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 439 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS B 471 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 441 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 468 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY B 494 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 470 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 160 through 161 removed outlier: 4.083A pdb=" N SER C 10 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU C 7 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU C 35 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 9 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE C 60 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 193 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 62 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU C 186 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ARG C 192 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.515A pdb=" N LYS C 260 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA C 351 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS C 265 " --> pdb=" O ARG C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.515A pdb=" N LYS C 260 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA C 351 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL C 437 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU C 398 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL C 439 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU C 400 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 441 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 402 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY C 443 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG C 404 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 437 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR C 469 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 439 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N HIS C 471 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 441 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 468 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY C 494 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 470 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU C 493 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 161 through 163 removed outlier: 6.882A pdb=" N ARG D 96 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE D 124 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL D 98 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS D 6 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N CYS D 99 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE D 8 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU D 7 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 35 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 9 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL D 32 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR D 61 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 34 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL D 63 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR D 36 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU D 186 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ARG D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 260 through 266 removed outlier: 6.030A pdb=" N LYS D 260 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 350 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS D 264 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG D 354 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N HIS D 266 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS D 395 " --> pdb=" O CYS D 349 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N VAL D 396 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N GLY D 438 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU D 398 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP D 440 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 400 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA D 442 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA D 402 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL D 437 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR D 469 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 439 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS D 471 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 441 " --> pdb=" O HIS D 471 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL D 468 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLY D 494 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D 470 " --> pdb=" O GLY D 494 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 493 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 160 through 161 removed outlier: 6.417A pdb=" N VAL E 98 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 7 " --> pdb=" O HIS E 33 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU E 35 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 9 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 60 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL E 193 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG E 62 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 185 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN E 194 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL E 183 " --> pdb=" O GLN E 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 260 through 266 removed outlier: 6.027A pdb=" N LYS E 260 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 350 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS E 264 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG E 354 " --> pdb=" O HIS E 264 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS E 266 " --> pdb=" O ARG E 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS E 395 " --> pdb=" O CYS E 349 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL E 437 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU E 398 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL E 439 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU E 400 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU E 441 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA E 402 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY E 443 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG E 404 " --> pdb=" O GLY E 443 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E 467 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLY E 443 " --> pdb=" O HIS E 471 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL E 468 " --> pdb=" O ARG E 492 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY E 494 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 470 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU E 493 " --> pdb=" O GLU E 517 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.929A pdb=" N SER F 10 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 32 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR F 61 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL F 34 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL F 63 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR F 36 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 60 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL F 193 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG F 62 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU F 186 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG F 192 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 260 through 261 removed outlier: 7.637A pdb=" N LYS F 260 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA F 351 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS F 265 " --> pdb=" O ARG F 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 260 through 261 removed outlier: 7.637A pdb=" N LYS F 260 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA F 351 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL F 436 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 398 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY F 438 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 437 " --> pdb=" O ALA F 467 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR F 469 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL F 439 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS F 471 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU F 441 " --> pdb=" O HIS F 471 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL F 468 " --> pdb=" O ARG F 492 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLY F 494 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL F 470 " --> pdb=" O GLY F 494 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 493 " --> pdb=" O GLU F 517 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3726 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: 11.36 Time building geometry restraints manager: 8.05 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: 7642 1.33 - 1.45: 5637 1.45 - 1.57: 16728 1.57 - 1.69: 63 1.69 - 1.81: 174 Bond restraints: 30244 Sorted by residual: bond pdb=" C LEU C 493 " pdb=" N GLY C 494 " ideal model delta sigma weight residual 1.332 1.315 0.017 5.00e-03 4.00e+04 1.22e+01 bond pdb=" C ARG F 297 " pdb=" N LEU F 298 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.47e-02 4.63e+03 1.04e+01 bond pdb=" C VAL A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.23e-02 6.61e+03 9.76e+00 bond pdb=" CA VAL A 18 " pdb=" CB VAL A 18 " ideal model delta sigma weight residual 1.539 1.551 -0.012 5.40e-03 3.43e+04 5.27e+00 bond pdb=" C ARG E 39 " pdb=" N PRO E 40 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.44e-02 4.82e+03 3.85e+00 ... (remaining 30239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 40518 2.39 - 4.77: 631 4.77 - 7.16: 87 7.16 - 9.54: 12 9.54 - 11.93: 1 Bond angle restraints: 41249 Sorted by residual: angle pdb=" C ARG F 297 " pdb=" N LEU F 298 " pdb=" CA LEU F 298 " ideal model delta sigma weight residual 120.68 132.61 -11.93 1.52e+00 4.33e-01 6.16e+01 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 113.71 107.54 6.17 9.50e-01 1.11e+00 4.22e+01 angle pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" C VAL B 363 " ideal model delta sigma weight residual 113.71 107.86 5.85 9.50e-01 1.11e+00 3.80e+01 angle pdb=" N GLU C 177 " pdb=" CA GLU C 177 " pdb=" C GLU C 177 " ideal model delta sigma weight residual 114.56 107.73 6.83 1.27e+00 6.20e-01 2.89e+01 angle pdb=" C VAL D 56 " pdb=" N ASN D 57 " pdb=" CA ASN D 57 " ideal model delta sigma weight residual 122.82 130.10 -7.28 1.42e+00 4.96e-01 2.63e+01 ... (remaining 41244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 16622 22.39 - 44.78: 1407 44.78 - 67.17: 102 67.17 - 89.56: 40 89.56 - 111.94: 2 Dihedral angle restraints: 18173 sinusoidal: 7626 harmonic: 10547 Sorted by residual: dihedral pdb=" CA VAL C 63 " pdb=" C VAL C 63 " pdb=" N ALA C 64 " pdb=" CA ALA C 64 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA MET B 140 " pdb=" C MET B 140 " pdb=" N PRO B 141 " pdb=" CA PRO B 141 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLU E 177 " pdb=" C GLU E 177 " pdb=" N GLN E 178 " pdb=" CA GLN E 178 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 18170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3843 0.061 - 0.121: 605 0.121 - 0.182: 43 0.182 - 0.243: 16 0.243 - 0.303: 15 Chirality restraints: 4522 Sorted by residual: chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' ATP D 701 " pdb=" C2' ATP D 701 " pdb=" C4' ATP D 701 " pdb=" O3' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" C4' ATP A 701 " pdb=" O3' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4519 not shown) Planarity restraints: 5365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 221 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO F 222 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 221 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO E 222 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 221 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 222 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 222 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 222 " -0.033 5.00e-02 4.00e+02 ... (remaining 5362 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 274 2.56 - 3.15: 25006 3.15 - 3.73: 49097 3.73 - 4.32: 64691 4.32 - 4.90: 106833 Nonbonded interactions: 245901 Sorted by model distance: nonbonded pdb=" O2B ATP D 701 " pdb="MG MG D 702 " model vdw 1.981 2.170 nonbonded pdb=" O3B ATP C 701 " pdb="MG MG C 702 " model vdw 2.009 2.170 nonbonded pdb=" O2G ATP D 701 " pdb="MG MG D 702 " model vdw 2.011 2.170 nonbonded pdb=" OG1 THR B 593 " pdb=" OD2 ASP B 596 " model vdw 2.106 3.040 nonbonded pdb=" OG1 THR E 593 " pdb=" OD2 ASP E 596 " model vdw 2.112 3.040 ... (remaining 245896 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' and (resid 2 through 534 or resid 551 through 629 or resid 701)) selection = (chain 'B' and (resid 2 through 534 or resid 551 through 629 or resid 701)) selection = (chain 'C' and (resid 2 through 534 or resid 551 through 629 or resid 701)) selection = (chain 'D' and (resid 2 through 534 or resid 551 through 629 or resid 701)) selection = (chain 'E' and (resid 2 through 534 or resid 551 through 629 or resid 701)) selection = (chain 'F' and (resid 2 through 629 or resid 701)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 7.020 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: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 70.080 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.004 0.287 30261 Z= 0.168 Angle : 0.711 11.929 41249 Z= 0.388 Chirality : 0.047 0.303 4522 Planarity : 0.006 0.077 5365 Dihedral : 15.004 111.944 11361 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.80 % Favored : 93.01 % Rotamer: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3663 helix: 0.84 (0.12), residues: 1668 sheet: -0.50 (0.24), residues: 480 loop : -1.81 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 239 HIS 0.013 0.001 HIS C 417 PHE 0.038 0.002 PHE A 83 TYR 0.021 0.002 TYR A 444 ARG 0.010 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.15830 ( 1305) hydrogen bonds : angle 6.22987 ( 3726) metal coordination : bond 0.06960 ( 17) covalent geometry : bond 0.00327 (30244) covalent geometry : angle 0.71078 (41249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7911 (ttm) cc_final: 0.7659 (ttm) REVERT: A 316 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8534 (tptt) REVERT: A 340 TYR cc_start: 0.8807 (t80) cc_final: 0.8555 (t80) REVERT: A 447 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6201 (tm-30) REVERT: A 453 TYR cc_start: 0.7772 (m-80) cc_final: 0.7279 (m-80) REVERT: B 453 TYR cc_start: 0.7481 (m-80) cc_final: 0.6980 (m-80) REVERT: D 86 PHE cc_start: 0.7567 (m-10) cc_final: 0.7269 (m-10) REVERT: D 316 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8884 (mmmm) REVERT: D 447 GLU cc_start: 0.8584 (mp0) cc_final: 0.8103 (tm-30) REVERT: E 112 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 197 ASP cc_start: 0.8076 (p0) cc_final: 0.7535 (p0) REVERT: E 453 TYR cc_start: 0.8379 (m-80) cc_final: 0.8096 (m-80) REVERT: F 315 MET cc_start: 0.8485 (mtt) cc_final: 0.8212 (mmm) outliers start: 5 outliers final: 1 residues processed: 142 average time/residue: 0.5863 time to fit residues: 121.2660 Evaluate side-chains 104 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 287 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 0.0870 chunk 214 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 136 GLN A 154 GLN A 178 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 581 ASN ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 471 HIS ** D 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS E 154 GLN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN ** E 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 209 GLN F 264 HIS F 346 GLN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.053875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044878 restraints weight = 148657.880| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.40 r_work: 0.3049 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 30261 Z= 0.160 Angle : 0.672 12.095 41249 Z= 0.338 Chirality : 0.044 0.174 4522 Planarity : 0.005 0.058 5365 Dihedral : 8.464 112.393 4514 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 0.61 % Allowed : 7.07 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3663 helix: 1.21 (0.13), residues: 1673 sheet: -0.39 (0.26), residues: 416 loop : -1.62 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 239 HIS 0.010 0.001 HIS D 156 PHE 0.021 0.002 PHE F 48 TYR 0.019 0.001 TYR C 521 ARG 0.012 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1305) hydrogen bonds : angle 4.82125 ( 3726) metal coordination : bond 0.07879 ( 17) covalent geometry : bond 0.00345 (30244) covalent geometry : angle 0.67189 (41249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.8155 (mptt) cc_final: 0.7944 (mmtm) REVERT: A 314 TYR cc_start: 0.7329 (t80) cc_final: 0.6873 (t80) REVERT: A 316 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8783 (tptt) REVERT: A 340 TYR cc_start: 0.8761 (t80) cc_final: 0.8469 (t80) REVERT: A 447 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6356 (tm-30) REVERT: A 453 TYR cc_start: 0.7648 (m-80) cc_final: 0.7258 (m-10) REVERT: B 453 TYR cc_start: 0.7476 (m-80) cc_final: 0.7013 (m-10) REVERT: C 140 MET cc_start: 0.7634 (tmm) cc_final: 0.7227 (tmm) REVERT: D 187 LYS cc_start: 0.8204 (pptt) cc_final: 0.7959 (pptt) REVERT: D 316 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8954 (mmmm) REVERT: D 447 GLU cc_start: 0.8570 (mp0) cc_final: 0.8178 (tm-30) REVERT: E 197 ASP cc_start: 0.8087 (p0) cc_final: 0.7528 (p0) REVERT: F 205 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (pp30) REVERT: F 231 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (p) REVERT: F 314 TYR cc_start: 0.6838 (t80) cc_final: 0.6554 (t80) REVERT: F 315 MET cc_start: 0.8460 (mtt) cc_final: 0.8070 (mmm) outliers start: 18 outliers final: 4 residues processed: 129 average time/residue: 0.5460 time to fit residues: 105.4166 Evaluate side-chains 107 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 299 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 601 GLN D 136 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043553 restraints weight = 149659.647| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.44 r_work: 0.2997 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30261 Z= 0.165 Angle : 0.627 11.513 41249 Z= 0.317 Chirality : 0.043 0.175 4522 Planarity : 0.005 0.053 5365 Dihedral : 8.213 110.273 4512 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.50 % Rotamer: Outliers : 1.15 % Allowed : 9.30 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3663 helix: 1.39 (0.13), residues: 1674 sheet: -0.36 (0.25), residues: 446 loop : -1.61 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 302 HIS 0.011 0.001 HIS D 156 PHE 0.036 0.002 PHE A 179 TYR 0.023 0.001 TYR C 521 ARG 0.005 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1305) hydrogen bonds : angle 4.46741 ( 3726) metal coordination : bond 0.00541 ( 17) covalent geometry : bond 0.00385 (30244) covalent geometry : angle 0.62712 (41249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: A 314 TYR cc_start: 0.7364 (t80) cc_final: 0.6945 (t80) REVERT: A 315 MET cc_start: 0.7727 (mmm) cc_final: 0.7525 (mmm) REVERT: A 316 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8831 (tptt) REVERT: A 447 GLU cc_start: 0.6558 (tm-30) cc_final: 0.6170 (tm-30) REVERT: A 453 TYR cc_start: 0.7698 (m-80) cc_final: 0.7284 (m-10) REVERT: B 315 MET cc_start: 0.8828 (mmm) cc_final: 0.8589 (mtt) REVERT: C 316 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8649 (mmtm) REVERT: C 584 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8892 (tt) REVERT: D 316 LYS cc_start: 0.9332 (mtpt) cc_final: 0.8983 (mmmm) REVERT: D 447 GLU cc_start: 0.8641 (mp0) cc_final: 0.8256 (tm-30) REVERT: E 138 ARG cc_start: 0.7508 (tpp-160) cc_final: 0.7067 (tpp-160) REVERT: E 197 ASP cc_start: 0.8181 (p0) cc_final: 0.7671 (p0) REVERT: E 315 MET cc_start: 0.8740 (mmm) cc_final: 0.8518 (mmp) REVERT: E 316 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8866 (mmmt) REVERT: F 220 MET cc_start: 0.9030 (ppp) cc_final: 0.8688 (ppp) REVERT: F 314 TYR cc_start: 0.6834 (t80) cc_final: 0.6565 (t80) REVERT: F 315 MET cc_start: 0.8407 (mtt) cc_final: 0.7982 (mmm) REVERT: F 316 LYS cc_start: 0.8861 (ptpt) cc_final: 0.8655 (pttm) outliers start: 34 outliers final: 10 residues processed: 131 average time/residue: 0.5277 time to fit residues: 104.3764 Evaluate side-chains 105 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 450 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain E residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 222 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 136 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.052491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043322 restraints weight = 151302.356| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.48 r_work: 0.2991 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30261 Z= 0.145 Angle : 0.601 11.896 41249 Z= 0.304 Chirality : 0.042 0.181 4522 Planarity : 0.005 0.052 5365 Dihedral : 8.071 107.560 4512 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.42 % Favored : 93.39 % Rotamer: Outliers : 1.31 % Allowed : 10.85 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3663 helix: 1.50 (0.13), residues: 1673 sheet: -0.58 (0.24), residues: 503 loop : -1.55 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 150 HIS 0.010 0.001 HIS D 156 PHE 0.016 0.001 PHE F 48 TYR 0.021 0.001 TYR A 444 ARG 0.004 0.000 ARG E 463 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 1305) hydrogen bonds : angle 4.31985 ( 3726) metal coordination : bond 0.00319 ( 17) covalent geometry : bond 0.00342 (30244) covalent geometry : angle 0.60096 (41249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (pp) REVERT: A 316 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8817 (tptp) REVERT: A 444 TYR cc_start: 0.8303 (t80) cc_final: 0.7927 (t80) REVERT: A 453 TYR cc_start: 0.7725 (m-80) cc_final: 0.7417 (m-10) REVERT: B 112 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9122 (tt0) REVERT: B 289 LYS cc_start: 0.8772 (pttp) cc_final: 0.8554 (pttp) REVERT: C 140 MET cc_start: 0.7765 (tmm) cc_final: 0.7379 (tmm) REVERT: D 316 LYS cc_start: 0.9321 (mtpt) cc_final: 0.9000 (mmmm) REVERT: D 447 GLU cc_start: 0.8657 (mp0) cc_final: 0.8309 (tm-30) REVERT: E 100 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9173 (pp) REVERT: E 107 MET cc_start: 0.8974 (mtp) cc_final: 0.8732 (ttp) REVERT: E 197 ASP cc_start: 0.8234 (p0) cc_final: 0.7685 (p0) REVERT: E 315 MET cc_start: 0.8747 (mmm) cc_final: 0.8485 (mmp) REVERT: F 111 MET cc_start: 0.8956 (ttm) cc_final: 0.8745 (ttm) REVERT: F 220 MET cc_start: 0.9024 (ppp) cc_final: 0.8779 (ppp) REVERT: F 223 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8055 (pp20) REVERT: F 314 TYR cc_start: 0.6894 (t80) cc_final: 0.6659 (t80) REVERT: F 315 MET cc_start: 0.8431 (mtt) cc_final: 0.7994 (mmm) outliers start: 39 outliers final: 15 residues processed: 138 average time/residue: 0.5063 time to fit residues: 105.7292 Evaluate side-chains 115 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 223 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 299 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 193 optimal weight: 0.9980 chunk 318 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN ** E 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 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 = 0.3418 r_free = 0.3418 target = 0.052561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043454 restraints weight = 149765.548| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.44 r_work: 0.2998 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30261 Z= 0.126 Angle : 0.585 11.967 41249 Z= 0.294 Chirality : 0.041 0.187 4522 Planarity : 0.004 0.051 5365 Dihedral : 7.943 105.218 4512 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 1.52 % Allowed : 11.99 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3663 helix: 1.58 (0.13), residues: 1673 sheet: -0.54 (0.24), residues: 491 loop : -1.52 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 150 HIS 0.009 0.001 HIS D 156 PHE 0.015 0.001 PHE F 48 TYR 0.019 0.001 TYR C 521 ARG 0.006 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1305) hydrogen bonds : angle 4.17488 ( 3726) metal coordination : bond 0.00290 ( 17) covalent geometry : bond 0.00300 (30244) covalent geometry : angle 0.58508 (41249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8225 (pp) REVERT: A 314 TYR cc_start: 0.7390 (t80) cc_final: 0.7005 (t80) REVERT: A 315 MET cc_start: 0.7955 (mmp) cc_final: 0.7552 (mmm) REVERT: A 316 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8817 (tptt) REVERT: A 444 TYR cc_start: 0.8325 (t80) cc_final: 0.7876 (t80) REVERT: A 453 TYR cc_start: 0.7674 (m-80) cc_final: 0.7394 (m-10) REVERT: B 112 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9099 (tt0) REVERT: C 316 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8694 (mmtm) REVERT: D 316 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9014 (mmmm) REVERT: D 447 GLU cc_start: 0.8642 (mp0) cc_final: 0.8241 (tm-30) REVERT: E 100 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9211 (pp) REVERT: E 197 ASP cc_start: 0.8239 (p0) cc_final: 0.7696 (p0) REVERT: E 315 MET cc_start: 0.8781 (mmm) cc_final: 0.8551 (mmp) REVERT: F 220 MET cc_start: 0.9015 (ppp) cc_final: 0.8780 (ppp) REVERT: F 223 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8032 (pp20) REVERT: F 314 TYR cc_start: 0.6914 (t80) cc_final: 0.6708 (t80) REVERT: F 315 MET cc_start: 0.8399 (mtt) cc_final: 0.7972 (mmm) outliers start: 45 outliers final: 22 residues processed: 137 average time/residue: 0.5162 time to fit residues: 107.6068 Evaluate side-chains 122 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 356 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 272 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS ** E 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.052213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.043109 restraints weight = 150948.745| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.40 r_work: 0.2986 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 30261 Z= 0.135 Angle : 0.582 11.915 41249 Z= 0.292 Chirality : 0.041 0.177 4522 Planarity : 0.004 0.050 5365 Dihedral : 7.760 101.860 4512 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 1.68 % Allowed : 12.87 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3663 helix: 1.71 (0.13), residues: 1668 sheet: -0.62 (0.24), residues: 502 loop : -1.41 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 150 HIS 0.010 0.001 HIS D 156 PHE 0.015 0.001 PHE C 78 TYR 0.016 0.001 TYR C 521 ARG 0.006 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 1305) hydrogen bonds : angle 4.12001 ( 3726) metal coordination : bond 0.03015 ( 17) covalent geometry : bond 0.00316 (30244) covalent geometry : angle 0.58182 (41249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 177 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: A 314 TYR cc_start: 0.7426 (t80) cc_final: 0.6990 (t80) REVERT: A 315 MET cc_start: 0.7965 (mmp) cc_final: 0.7531 (mmm) REVERT: A 316 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8833 (tptt) REVERT: A 453 TYR cc_start: 0.7628 (m-80) cc_final: 0.7350 (m-10) REVERT: B 112 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.9119 (tt0) REVERT: B 316 LYS cc_start: 0.9489 (mtpp) cc_final: 0.9284 (ttmm) REVERT: B 381 MET cc_start: 0.8473 (mmm) cc_final: 0.8230 (mtt) REVERT: C 140 MET cc_start: 0.7845 (tmm) cc_final: 0.7437 (tmm) REVERT: C 316 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8767 (mmtm) REVERT: C 444 TYR cc_start: 0.8735 (t80) cc_final: 0.8328 (t80) REVERT: D 316 LYS cc_start: 0.9356 (mtpt) cc_final: 0.9024 (mmmm) REVERT: D 447 GLU cc_start: 0.8668 (mp0) cc_final: 0.8276 (tm-30) REVERT: E 197 ASP cc_start: 0.8266 (p0) cc_final: 0.7709 (p0) REVERT: E 315 MET cc_start: 0.8765 (mmm) cc_final: 0.8501 (mmp) REVERT: F 220 MET cc_start: 0.9015 (ppp) cc_final: 0.8781 (ppp) REVERT: F 223 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8008 (pp20) REVERT: F 315 MET cc_start: 0.8406 (mtt) cc_final: 0.7980 (mmm) outliers start: 50 outliers final: 25 residues processed: 145 average time/residue: 0.4988 time to fit residues: 110.1775 Evaluate side-chains 125 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 195 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS E 567 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 614 GLN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.052042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042934 restraints weight = 150506.683| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.39 r_work: 0.2979 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30261 Z= 0.138 Angle : 0.593 12.819 41249 Z= 0.295 Chirality : 0.041 0.164 4522 Planarity : 0.004 0.050 5365 Dihedral : 7.630 99.804 4512 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.03 % Favored : 93.78 % Rotamer: Outliers : 1.82 % Allowed : 13.44 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3663 helix: 1.74 (0.13), residues: 1669 sheet: -0.63 (0.24), residues: 502 loop : -1.39 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 150 HIS 0.010 0.001 HIS D 156 PHE 0.016 0.001 PHE C 78 TYR 0.012 0.001 TYR C 521 ARG 0.007 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 1305) hydrogen bonds : angle 4.10079 ( 3726) metal coordination : bond 0.00265 ( 17) covalent geometry : bond 0.00328 (30244) covalent geometry : angle 0.59335 (41249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 177 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: A 314 TYR cc_start: 0.7400 (t80) cc_final: 0.6924 (t80) REVERT: A 315 MET cc_start: 0.8001 (mmp) cc_final: 0.7556 (mmm) REVERT: A 316 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8837 (tptt) REVERT: A 453 TYR cc_start: 0.7609 (m-80) cc_final: 0.7342 (m-10) REVERT: B 112 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.9124 (tt0) REVERT: B 139 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6044 (mm) REVERT: B 316 LYS cc_start: 0.9497 (mtpp) cc_final: 0.9293 (ttmm) REVERT: B 381 MET cc_start: 0.8532 (mmm) cc_final: 0.8196 (mtt) REVERT: C 316 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8800 (mmtm) REVERT: C 444 TYR cc_start: 0.8745 (t80) cc_final: 0.8341 (t80) REVERT: D 209 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: D 447 GLU cc_start: 0.8666 (mp0) cc_final: 0.8299 (tm-30) REVERT: E 138 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6428 (tpp-160) REVERT: E 162 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9047 (pp) REVERT: E 197 ASP cc_start: 0.8277 (p0) cc_final: 0.7721 (p0) REVERT: E 315 MET cc_start: 0.8759 (mmm) cc_final: 0.8498 (mmp) REVERT: E 567 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8581 (m110) REVERT: F 220 MET cc_start: 0.9001 (ppp) cc_final: 0.8754 (ppp) REVERT: F 223 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: F 315 MET cc_start: 0.8374 (mtt) cc_final: 0.7990 (mmm) outliers start: 54 outliers final: 26 residues processed: 144 average time/residue: 0.4842 time to fit residues: 108.5143 Evaluate side-chains 128 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 567 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 344 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS E 567 ASN F 178 GLN ** F 570 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 = 0.3378 r_free = 0.3378 target = 0.051412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042308 restraints weight = 151187.547| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.37 r_work: 0.2954 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30261 Z= 0.169 Angle : 0.609 11.731 41249 Z= 0.304 Chirality : 0.042 0.237 4522 Planarity : 0.004 0.050 5365 Dihedral : 7.556 97.524 4512 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.22 % Favored : 93.58 % Rotamer: Outliers : 1.65 % Allowed : 13.94 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3663 helix: 1.80 (0.13), residues: 1672 sheet: -0.69 (0.24), residues: 502 loop : -1.37 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 159 HIS 0.010 0.001 HIS D 156 PHE 0.017 0.001 PHE E 78 TYR 0.020 0.001 TYR A 444 ARG 0.007 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 1305) hydrogen bonds : angle 4.13839 ( 3726) metal coordination : bond 0.00325 ( 17) covalent geometry : bond 0.00397 (30244) covalent geometry : angle 0.60939 (41249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8463 (pp) REVERT: A 177 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5437 (mp0) REVERT: A 316 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8842 (tptp) REVERT: A 444 TYR cc_start: 0.8335 (t80) cc_final: 0.7936 (t80) REVERT: A 453 TYR cc_start: 0.7588 (m-80) cc_final: 0.7320 (m-10) REVERT: B 112 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.9143 (tt0) REVERT: B 139 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6076 (mm) REVERT: B 315 MET cc_start: 0.8710 (mpp) cc_final: 0.8483 (mpp) REVERT: C 316 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8823 (mmtm) REVERT: D 316 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9032 (mmmm) REVERT: D 447 GLU cc_start: 0.8685 (mp0) cc_final: 0.8343 (tm-30) REVERT: E 138 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6305 (tpp-160) REVERT: E 197 ASP cc_start: 0.8297 (p0) cc_final: 0.7679 (p0) REVERT: E 315 MET cc_start: 0.8749 (mmm) cc_final: 0.8491 (mmp) REVERT: E 453 TYR cc_start: 0.8281 (m-10) cc_final: 0.7967 (m-10) REVERT: E 567 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8586 (m-40) REVERT: F 82 MET cc_start: 0.9186 (ptm) cc_final: 0.8943 (ptt) REVERT: F 220 MET cc_start: 0.9013 (ppp) cc_final: 0.8753 (ppp) REVERT: F 223 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8026 (pp20) REVERT: F 315 MET cc_start: 0.8440 (mtt) cc_final: 0.8073 (mmm) outliers start: 49 outliers final: 27 residues processed: 140 average time/residue: 0.4883 time to fit residues: 105.2467 Evaluate side-chains 128 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 567 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 17 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 63 optimal weight: 0.0060 chunk 199 optimal weight: 0.4980 chunk 223 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 ASN ** F 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 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 = 0.3400 r_free = 0.3400 target = 0.052118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.043031 restraints weight = 148402.055| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.35 r_work: 0.2976 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30261 Z= 0.120 Angle : 0.603 12.166 41249 Z= 0.297 Chirality : 0.041 0.239 4522 Planarity : 0.004 0.051 5365 Dihedral : 7.414 94.809 4512 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.81 % Favored : 93.99 % Rotamer: Outliers : 1.48 % Allowed : 14.18 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3663 helix: 1.78 (0.13), residues: 1671 sheet: -0.67 (0.26), residues: 446 loop : -1.32 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 150 HIS 0.009 0.001 HIS D 156 PHE 0.017 0.001 PHE E 78 TYR 0.018 0.001 TYR A 444 ARG 0.006 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 1305) hydrogen bonds : angle 4.04151 ( 3726) metal coordination : bond 0.00244 ( 17) covalent geometry : bond 0.00285 (30244) covalent geometry : angle 0.60273 (41249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8467 (pp) REVERT: A 177 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5591 (mp0) REVERT: A 316 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8825 (tptp) REVERT: A 444 TYR cc_start: 0.8328 (t80) cc_final: 0.7914 (t80) REVERT: A 453 TYR cc_start: 0.7551 (m-80) cc_final: 0.7225 (m-10) REVERT: B 112 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.9124 (tt0) REVERT: B 139 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6081 (mm) REVERT: B 598 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9003 (mt) REVERT: C 316 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8807 (mmtm) REVERT: C 444 TYR cc_start: 0.8779 (t80) cc_final: 0.8402 (t80) REVERT: D 316 LYS cc_start: 0.9354 (ttmt) cc_final: 0.8990 (mmmm) REVERT: D 447 GLU cc_start: 0.8669 (mp0) cc_final: 0.8315 (tm-30) REVERT: E 138 ARG cc_start: 0.7014 (tpt170) cc_final: 0.6356 (tpp-160) REVERT: E 197 ASP cc_start: 0.8282 (p0) cc_final: 0.7673 (p0) REVERT: E 315 MET cc_start: 0.8718 (mmm) cc_final: 0.8441 (mmp) REVERT: E 453 TYR cc_start: 0.8344 (m-10) cc_final: 0.8030 (m-10) REVERT: E 567 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: F 82 MET cc_start: 0.9201 (ptm) cc_final: 0.8957 (ptt) REVERT: F 220 MET cc_start: 0.8997 (ppp) cc_final: 0.8743 (ppp) REVERT: F 223 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8034 (pp20) REVERT: F 315 MET cc_start: 0.8395 (mtt) cc_final: 0.8030 (mmm) outliers start: 44 outliers final: 27 residues processed: 139 average time/residue: 0.5359 time to fit residues: 114.3645 Evaluate side-chains 128 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 567 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 280 optimal weight: 0.7980 chunk 346 optimal weight: 5.9990 chunk 152 optimal weight: 0.0010 chunk 250 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 340 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 ASN ** F 570 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 = 0.3387 r_free = 0.3387 target = 0.051754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042674 restraints weight = 148872.449| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.34 r_work: 0.2965 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30261 Z= 0.140 Angle : 0.605 11.923 41249 Z= 0.300 Chirality : 0.041 0.220 4522 Planarity : 0.004 0.051 5365 Dihedral : 7.337 91.551 4512 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.20 % Favored : 93.61 % Rotamer: Outliers : 1.31 % Allowed : 14.42 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3663 helix: 1.84 (0.13), residues: 1663 sheet: -0.69 (0.26), residues: 446 loop : -1.30 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 150 HIS 0.010 0.001 HIS D 156 PHE 0.017 0.001 PHE C 78 TYR 0.018 0.001 TYR A 444 ARG 0.007 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 1305) hydrogen bonds : angle 4.04836 ( 3726) metal coordination : bond 0.00270 ( 17) covalent geometry : bond 0.00332 (30244) covalent geometry : angle 0.60508 (41249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8408 (tp30) cc_final: 0.8160 (tp30) REVERT: A 171 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8530 (pp) REVERT: A 177 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5835 (mp0) REVERT: A 316 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8840 (tptp) REVERT: A 444 TYR cc_start: 0.8312 (t80) cc_final: 0.7909 (t80) REVERT: A 453 TYR cc_start: 0.7552 (m-80) cc_final: 0.7228 (m-10) REVERT: B 112 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9148 (tt0) REVERT: B 139 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6116 (mm) REVERT: B 598 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9015 (mt) REVERT: C 316 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8829 (mmtm) REVERT: C 381 MET cc_start: 0.8719 (mmm) cc_final: 0.8467 (mtt) REVERT: D 316 LYS cc_start: 0.9363 (ttmt) cc_final: 0.9001 (mmmm) REVERT: D 447 GLU cc_start: 0.8658 (mp0) cc_final: 0.8336 (tm-30) REVERT: E 138 ARG cc_start: 0.7036 (tpt170) cc_final: 0.6488 (tpp-160) REVERT: E 197 ASP cc_start: 0.8283 (p0) cc_final: 0.7688 (p0) REVERT: E 315 MET cc_start: 0.8709 (mmm) cc_final: 0.8434 (mmp) REVERT: E 453 TYR cc_start: 0.8360 (m-10) cc_final: 0.8049 (m-10) REVERT: E 567 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8525 (m-40) REVERT: F 82 MET cc_start: 0.9186 (ptm) cc_final: 0.8943 (ptt) REVERT: F 220 MET cc_start: 0.9001 (ppp) cc_final: 0.8749 (ppp) REVERT: F 223 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8032 (pp20) REVERT: F 315 MET cc_start: 0.8418 (mtt) cc_final: 0.8047 (mmm) outliers start: 39 outliers final: 28 residues processed: 132 average time/residue: 0.4869 time to fit residues: 98.7539 Evaluate side-chains 129 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 567 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 351 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 ASN ** F 570 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 = 0.3378 r_free = 0.3378 target = 0.051490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042405 restraints weight = 148631.603| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.34 r_work: 0.2954 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30261 Z= 0.156 Angle : 0.612 11.867 41249 Z= 0.303 Chirality : 0.042 0.204 4522 Planarity : 0.004 0.051 5365 Dihedral : 7.322 88.663 4512 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.09 % Favored : 93.72 % Rotamer: Outliers : 1.38 % Allowed : 14.28 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3663 helix: 1.84 (0.13), residues: 1664 sheet: -0.71 (0.26), residues: 446 loop : -1.31 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP B 159 HIS 0.010 0.001 HIS D 156 PHE 0.018 0.001 PHE D 78 TYR 0.017 0.001 TYR A 444 ARG 0.007 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 1305) hydrogen bonds : angle 4.06309 ( 3726) metal coordination : bond 0.00270 ( 17) covalent geometry : bond 0.00370 (30244) covalent geometry : angle 0.61192 (41249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12465.52 seconds wall clock time: 217 minutes 43.12 seconds (13063.12 seconds total)