Starting phenix.real_space_refine on Fri Sep 19 09:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.map" model { file = "/net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efi_47974/09_2025/9efi_47974.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.076 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 15802 2.51 5 N 3908 2.21 5 O 4940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24710 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6179 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 20, 'TRANS': 755} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 6176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6176 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 755} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Restraints were copied for chains: C, D Time building chain proxies: 9.97, per 1000 atoms: 0.40 Number of scatterers: 24710 At special positions: 0 Unit cell: (174.041, 137.287, 180.527, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 4940 8.00 N 3908 7.00 C 15802 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: 2.00 Conformation dependent library (CDL) restraints added in 901.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 50 sheets defined 35.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 45 through 75 Processing helix chain 'A' and resid 81 through 135 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.515A pdb=" N CYS A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 194 removed outlier: 4.787A pdb=" N ALA A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 removed outlier: 5.404A pdb=" N GLU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.585A pdb=" N HIS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 267 through 298 Processing helix chain 'A' and resid 304 through 323 Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.594A pdb=" N PHE A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.609A pdb=" N TYR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 52 through 76 removed outlier: 3.894A pdb=" N ASP B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 114 Processing helix chain 'B' and resid 115 through 137 removed outlier: 3.927A pdb=" N GLN B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 3.765A pdb=" N VAL B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 167 through 193 Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 267 through 297 Processing helix chain 'B' and resid 304 through 323 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.907A pdb=" N LEU B 389 " --> pdb=" O HIS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 514 through 523 removed outlier: 3.572A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 38 Processing helix chain 'C' and resid 45 through 75 Processing helix chain 'C' and resid 81 through 135 Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.515A pdb=" N CYS C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 194 removed outlier: 4.787A pdb=" N ALA C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 222 removed outlier: 5.405A pdb=" N GLU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.585A pdb=" N HIS C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 267 through 298 Processing helix chain 'C' and resid 304 through 323 Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.594A pdb=" N PHE C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.609A pdb=" N TYR C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 38 Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.894A pdb=" N ASP D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 114 Processing helix chain 'D' and resid 115 through 137 removed outlier: 3.927A pdb=" N GLN D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 removed outlier: 3.764A pdb=" N VAL D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 167 through 193 Processing helix chain 'D' and resid 203 through 222 Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 267 through 297 Processing helix chain 'D' and resid 304 through 323 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 385 through 389 removed outlier: 3.906A pdb=" N LEU D 389 " --> pdb=" O HIS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 514 through 523 removed outlier: 3.571A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.909A pdb=" N SER A 495 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 339 removed outlier: 5.290A pdb=" N LEU A 358 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 376 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 360 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLU A 391 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS A 672 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 393 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 339 removed outlier: 5.290A pdb=" N LEU A 358 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 376 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 360 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLU A 391 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS A 672 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 393 " --> pdb=" O LYS A 672 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY A 663 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS A 606 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN A 665 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 604 " --> pdb=" O ASN A 665 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A 598 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 597 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR A 640 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 599 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 638 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 601 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 636 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR A 603 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 634 " --> pdb=" O TYR A 603 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 605 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU A 632 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 349 removed outlier: 5.444A pdb=" N ILE A 423 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN A 442 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 425 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 349 removed outlier: 5.444A pdb=" N ILE A 423 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN A 442 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 425 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 437 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 692 Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AB1, first strand: chain 'A' and resid 714 through 715 removed outlier: 3.674A pdb=" N PHE A 772 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 747 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 758 through 759 Processing sheet with id=AB3, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.862A pdb=" N SER A 791 " --> pdb=" O SER A 726 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'B' and resid 330 through 331 removed outlier: 3.848A pdb=" N SER B 495 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 335 through 339 Processing sheet with id=AB7, first strand: chain 'B' and resid 346 through 349 removed outlier: 5.399A pdb=" N ILE B 423 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 442 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 346 through 349 removed outlier: 5.399A pdb=" N ILE B 423 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 442 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR B 437 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.533A pdb=" N TYR B 374 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 361 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS B 372 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE B 363 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 370 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 375 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 563 through 565 Processing sheet with id=AC2, first strand: chain 'B' and resid 585 through 588 Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 588 removed outlier: 3.875A pdb=" N LYS B 614 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 639 through 640 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.533A pdb=" N GLN B 713 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B 772 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 747 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN B 740 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 745 " --> pdb=" O ASN B 740 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 758 through 759 Processing sheet with id=AC7, first strand: chain 'B' and resid 758 through 759 removed outlier: 4.731A pdb=" N THR B 722 " --> pdb=" O LYS B 795 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 728 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP B 789 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER B 730 " --> pdb=" O PHE B 787 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N PHE B 787 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AC9, first strand: chain 'C' and resid 330 through 331 removed outlier: 3.909A pdb=" N SER C 495 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 335 through 339 removed outlier: 5.289A pdb=" N LEU C 358 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 376 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 360 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLU C 391 " --> pdb=" O GLU C 670 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS C 672 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 393 " --> pdb=" O LYS C 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 335 through 339 removed outlier: 5.289A pdb=" N LEU C 358 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 376 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 360 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLU C 391 " --> pdb=" O GLU C 670 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS C 672 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 393 " --> pdb=" O LYS C 672 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY C 663 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS C 606 " --> pdb=" O GLY C 663 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN C 665 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR C 604 " --> pdb=" O ASN C 665 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP C 598 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 597 " --> pdb=" O TYR C 640 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR C 640 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR C 599 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 638 " --> pdb=" O TYR C 599 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 601 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 636 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR C 603 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 634 " --> pdb=" O TYR C 603 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 605 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C 632 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 346 through 349 removed outlier: 5.444A pdb=" N ILE C 423 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN C 442 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 425 " --> pdb=" O THR C 440 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 346 through 349 removed outlier: 5.444A pdb=" N ILE C 423 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN C 442 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 425 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR C 437 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AD6, first strand: chain 'C' and resid 689 through 692 Processing sheet with id=AD7, first strand: chain 'C' and resid 694 through 697 Processing sheet with id=AD8, first strand: chain 'C' and resid 714 through 715 removed outlier: 3.675A pdb=" N PHE C 772 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 747 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 758 through 759 Processing sheet with id=AE1, first strand: chain 'C' and resid 758 through 759 removed outlier: 3.862A pdb=" N SER C 791 " --> pdb=" O SER C 726 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AE3, first strand: chain 'D' and resid 330 through 331 removed outlier: 3.848A pdb=" N SER D 495 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 335 through 339 Processing sheet with id=AE5, first strand: chain 'D' and resid 346 through 349 removed outlier: 5.399A pdb=" N ILE D 423 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN D 442 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 346 through 349 removed outlier: 5.399A pdb=" N ILE D 423 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN D 442 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR D 437 " --> pdb=" O TYR D 411 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 357 through 364 removed outlier: 6.533A pdb=" N TYR D 374 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 361 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS D 372 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 363 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 370 " --> pdb=" O ILE D 363 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 375 " --> pdb=" O SER D 390 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 563 through 565 Processing sheet with id=AE9, first strand: chain 'D' and resid 585 through 588 Processing sheet with id=AF1, first strand: chain 'D' and resid 585 through 588 removed outlier: 3.875A pdb=" N LYS D 614 " --> pdb=" O HIS D 650 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 639 through 640 Processing sheet with id=AF3, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.534A pdb=" N GLN D 713 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE D 772 " --> pdb=" O LEU D 715 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE D 747 " --> pdb=" O ILE D 738 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN D 740 " --> pdb=" O VAL D 745 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 745 " --> pdb=" O ASN D 740 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AF5, first strand: chain 'D' and resid 758 through 759 removed outlier: 4.731A pdb=" N THR D 722 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D 728 " --> pdb=" O ASP D 789 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP D 789 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER D 730 " --> pdb=" O PHE D 787 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE D 787 " --> pdb=" O SER D 730 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3672 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: 5.61 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7954 1.34 - 1.46: 5122 1.46 - 1.58: 12006 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 25174 Sorted by residual: bond pdb=" N LYS B 575 " pdb=" CA LYS B 575 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.20e-01 bond pdb=" C LEU C 79 " pdb=" N ASN C 80 " ideal model delta sigma weight residual 1.325 1.335 -0.011 1.14e-02 7.69e+03 8.60e-01 bond pdb=" C LYS D 616 " pdb=" O LYS D 616 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.50e-03 1.11e+04 7.68e-01 bond pdb=" C LEU A 79 " pdb=" N ASN A 80 " ideal model delta sigma weight residual 1.325 1.335 -0.010 1.14e-02 7.69e+03 7.27e-01 bond pdb=" CA ILE B 154 " pdb=" CB ILE B 154 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 7.25e-01 ... (remaining 25169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 33709 1.47 - 2.94: 323 2.94 - 4.41: 44 4.41 - 5.88: 22 5.88 - 7.35: 2 Bond angle restraints: 34100 Sorted by residual: angle pdb=" C LYS D 616 " pdb=" CA LYS D 616 " pdb=" CB LYS D 616 " ideal model delta sigma weight residual 117.23 109.88 7.35 1.36e+00 5.41e-01 2.92e+01 angle pdb=" C LYS B 616 " pdb=" CA LYS B 616 " pdb=" CB LYS B 616 " ideal model delta sigma weight residual 117.23 109.92 7.31 1.36e+00 5.41e-01 2.89e+01 angle pdb=" C ASN C 80 " pdb=" CA ASN C 80 " pdb=" CB ASN C 80 " ideal model delta sigma weight residual 115.79 110.19 5.60 1.19e+00 7.06e-01 2.21e+01 angle pdb=" C ASN A 80 " pdb=" CA ASN A 80 " pdb=" CB ASN A 80 " ideal model delta sigma weight residual 115.79 110.19 5.60 1.19e+00 7.06e-01 2.21e+01 angle pdb=" CA LYS D 616 " pdb=" C LYS D 616 " pdb=" N ASN D 617 " ideal model delta sigma weight residual 119.98 116.70 3.28 8.50e-01 1.38e+00 1.49e+01 ... (remaining 34095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 14375 16.73 - 33.46: 553 33.46 - 50.19: 142 50.19 - 66.91: 12 66.91 - 83.64: 10 Dihedral angle restraints: 15092 sinusoidal: 5980 harmonic: 9112 Sorted by residual: dihedral pdb=" CA SER D 574 " pdb=" C SER D 574 " pdb=" N LYS D 575 " pdb=" CA LYS D 575 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER B 574 " pdb=" C SER B 574 " pdb=" N LYS B 575 " pdb=" CA LYS B 575 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ILE D 737 " pdb=" C ILE D 737 " pdb=" N ILE D 738 " pdb=" CA ILE D 738 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 15089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2459 0.029 - 0.057: 941 0.057 - 0.086: 256 0.086 - 0.114: 191 0.114 - 0.143: 51 Chirality restraints: 3898 Sorted by residual: chirality pdb=" CA VAL D 736 " pdb=" N VAL D 736 " pdb=" C VAL D 736 " pdb=" CB VAL D 736 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL B 736 " pdb=" N VAL B 736 " pdb=" C VAL B 736 " pdb=" CB VAL B 736 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 392 " pdb=" N ILE C 392 " pdb=" C ILE C 392 " pdb=" CB ILE C 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 3895 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 333 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO A 334 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 333 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO C 334 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 333 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO B 334 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " -0.016 5.00e-02 4.00e+02 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2560 2.75 - 3.29: 25632 3.29 - 3.82: 42163 3.82 - 4.36: 50127 4.36 - 4.90: 86601 Nonbonded interactions: 207083 Sorted by model distance: nonbonded pdb=" OG SER D 124 " pdb=" OE2 GLU D 189 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 124 " pdb=" OE2 GLU B 189 " model vdw 2.212 3.040 nonbonded pdb=" O LYS D 413 " pdb=" OH TYR D 437 " model vdw 2.231 3.040 nonbonded pdb=" O LYS B 413 " pdb=" OH TYR B 437 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 718 " pdb=" OH TYR B 723 " model vdw 2.258 3.040 ... (remaining 207078 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.470 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.400 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25174 Z= 0.091 Angle : 0.424 7.354 34100 Z= 0.235 Chirality : 0.039 0.143 3898 Planarity : 0.003 0.034 4372 Dihedral : 9.980 83.643 9228 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 2.55 % Allowed : 7.14 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 3088 helix: 3.09 (0.16), residues: 1004 sheet: 0.08 (0.20), residues: 762 loop : -1.63 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 516 TYR 0.009 0.001 TYR A 115 PHE 0.010 0.001 PHE B 235 TRP 0.006 0.001 TRP C 546 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00181 (25174) covalent geometry : angle 0.42433 (34100) hydrogen bonds : bond 0.12829 ( 1224) hydrogen bonds : angle 5.86408 ( 3672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 475 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.8058 (t80) cc_final: 0.7796 (t80) REVERT: A 58 ASP cc_start: 0.8457 (t0) cc_final: 0.8234 (t0) REVERT: A 83 LEU cc_start: 0.8712 (tp) cc_final: 0.8436 (tm) REVERT: A 89 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7376 (ttpp) REVERT: A 93 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 152 ASP cc_start: 0.8255 (t0) cc_final: 0.7773 (t0) REVERT: A 205 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7430 (p0) REVERT: A 208 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7707 (mt-10) REVERT: A 215 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 225 MET cc_start: 0.7114 (ttp) cc_final: 0.6402 (ttt) REVERT: A 243 ASN cc_start: 0.8545 (p0) cc_final: 0.7911 (p0) REVERT: A 251 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7635 (mttp) REVERT: A 255 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: A 338 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8529 (tppt) REVERT: A 455 GLU cc_start: 0.7667 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 467 TYR cc_start: 0.8912 (p90) cc_final: 0.8224 (p90) REVERT: A 497 GLU cc_start: 0.8162 (pt0) cc_final: 0.7954 (pt0) REVERT: A 499 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 528 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 551 ASP cc_start: 0.8771 (m-30) cc_final: 0.7932 (p0) REVERT: A 597 THR cc_start: 0.7930 (m) cc_final: 0.7067 (p) REVERT: A 638 VAL cc_start: 0.8635 (m) cc_final: 0.8425 (p) REVERT: A 670 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 747 PHE cc_start: 0.6857 (t80) cc_final: 0.6320 (t80) REVERT: A 756 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.5657 (t80) REVERT: B 45 THR cc_start: 0.8845 (m) cc_final: 0.8101 (m) REVERT: B 64 GLU cc_start: 0.8280 (tp30) cc_final: 0.8072 (tm-30) REVERT: B 138 GLU cc_start: 0.8044 (tp30) cc_final: 0.7758 (tp30) REVERT: B 261 GLU cc_start: 0.8901 (mp0) cc_final: 0.8571 (mp0) REVERT: B 285 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8602 (mtpp) REVERT: B 330 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8575 (mtpm) REVERT: B 379 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8037 (ttmm) REVERT: B 387 GLN cc_start: 0.9115 (mt0) cc_final: 0.8808 (mm-40) REVERT: B 467 TYR cc_start: 0.9029 (p90) cc_final: 0.8821 (p90) REVERT: B 499 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 611 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 650 HIS cc_start: 0.5968 (p90) cc_final: 0.5477 (p-80) REVERT: B 689 ILE cc_start: 0.5270 (OUTLIER) cc_final: 0.4795 (tp) REVERT: B 756 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.4984 (t80) REVERT: B 792 MET cc_start: 0.8687 (ttm) cc_final: 0.8237 (ttm) REVERT: C 57 TYR cc_start: 0.8054 (t80) cc_final: 0.7767 (t80) REVERT: C 58 ASP cc_start: 0.8451 (t0) cc_final: 0.8225 (t0) REVERT: C 83 LEU cc_start: 0.8733 (tp) cc_final: 0.8458 (tm) REVERT: C 89 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7384 (ttpp) REVERT: C 93 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 152 ASP cc_start: 0.8260 (t0) cc_final: 0.7780 (t0) REVERT: C 205 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7431 (p0) REVERT: C 208 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7711 (mt-10) REVERT: C 215 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7822 (mm-30) REVERT: C 225 MET cc_start: 0.7100 (ttp) cc_final: 0.6394 (ttt) REVERT: C 251 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7625 (mttp) REVERT: C 255 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: C 338 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8528 (tppt) REVERT: C 455 GLU cc_start: 0.7655 (tt0) cc_final: 0.7255 (tm-30) REVERT: C 467 TYR cc_start: 0.8925 (p90) cc_final: 0.8139 (p90) REVERT: C 497 GLU cc_start: 0.8170 (pt0) cc_final: 0.7962 (pt0) REVERT: C 499 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 551 ASP cc_start: 0.8788 (m-30) cc_final: 0.7971 (p0) REVERT: C 553 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6947 (pp) REVERT: C 597 THR cc_start: 0.7931 (m) cc_final: 0.7067 (p) REVERT: C 638 VAL cc_start: 0.8643 (m) cc_final: 0.8433 (p) REVERT: C 650 HIS cc_start: 0.6515 (p-80) cc_final: 0.6227 (p-80) REVERT: C 670 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 737 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.6148 (tp) REVERT: C 747 PHE cc_start: 0.6878 (t80) cc_final: 0.6333 (t80) REVERT: C 756 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5516 (t80) REVERT: D 45 THR cc_start: 0.8850 (m) cc_final: 0.8110 (m) REVERT: D 64 GLU cc_start: 0.8326 (tp30) cc_final: 0.8116 (tm-30) REVERT: D 138 GLU cc_start: 0.8041 (tp30) cc_final: 0.7751 (tp30) REVERT: D 261 GLU cc_start: 0.8890 (mp0) cc_final: 0.8559 (mp0) REVERT: D 285 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8607 (mtpp) REVERT: D 330 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8569 (mtpm) REVERT: D 379 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8033 (ttmm) REVERT: D 387 GLN cc_start: 0.9116 (mt0) cc_final: 0.8804 (mm-40) REVERT: D 467 TYR cc_start: 0.9040 (p90) cc_final: 0.8835 (p90) REVERT: D 499 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 611 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8154 (mm) REVERT: D 650 HIS cc_start: 0.5968 (p90) cc_final: 0.5476 (p-80) REVERT: D 756 TYR cc_start: 0.5314 (OUTLIER) cc_final: 0.4986 (t80) REVERT: D 792 MET cc_start: 0.8684 (ttm) cc_final: 0.8250 (ttm) outliers start: 71 outliers final: 2 residues processed: 526 average time/residue: 0.5769 time to fit residues: 353.1068 Evaluate side-chains 301 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 284 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 143 GLN A 223 ASN A 380 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A 753 GLN B 20 ASN B 76 GLN B 94 GLN B 95 ASN B 136 GLN B 172 GLN B 464 GLN B 541 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 587 GLN B 617 ASN ** B 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 143 GLN C 223 ASN C 380 GLN C 541 ASN C 724 ASN C 753 GLN D 20 ASN D 76 GLN D 94 GLN D 95 ASN D 136 GLN D 172 GLN D 464 GLN D 541 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 587 GLN D 617 ASN ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.144530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090185 restraints weight = 38420.389| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.98 r_work: 0.3152 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25174 Z= 0.121 Angle : 0.540 9.071 34100 Z= 0.283 Chirality : 0.042 0.241 3898 Planarity : 0.003 0.035 4372 Dihedral : 5.136 63.640 3340 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.55 % Rotamer: Outliers : 2.94 % Allowed : 11.99 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.16), residues: 3088 helix: 3.07 (0.16), residues: 1014 sheet: 0.13 (0.20), residues: 748 loop : -1.64 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 193 TYR 0.024 0.001 TYR A 115 PHE 0.013 0.001 PHE B 578 TRP 0.024 0.001 TRP B 662 HIS 0.004 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00268 (25174) covalent geometry : angle 0.54017 (34100) hydrogen bonds : bond 0.03653 ( 1224) hydrogen bonds : angle 4.66405 ( 3672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8187 (tp30) cc_final: 0.7875 (tt0) REVERT: A 57 TYR cc_start: 0.8069 (t80) cc_final: 0.7816 (t80) REVERT: A 58 ASP cc_start: 0.8437 (t0) cc_final: 0.8198 (t0) REVERT: A 83 LEU cc_start: 0.8662 (tp) cc_final: 0.8393 (tm) REVERT: A 152 ASP cc_start: 0.8219 (t0) cc_final: 0.7693 (t0) REVERT: A 208 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7750 (mt-10) REVERT: A 215 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 243 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 251 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7126 (mttp) REVERT: A 255 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: A 338 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8524 (tppt) REVERT: A 467 TYR cc_start: 0.8716 (p90) cc_final: 0.8079 (p90) REVERT: A 499 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 528 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8566 (mm-30) REVERT: A 551 ASP cc_start: 0.8873 (m-30) cc_final: 0.7984 (p0) REVERT: A 622 MET cc_start: 0.6119 (mtm) cc_final: 0.5885 (mtm) REVERT: A 670 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 674 PHE cc_start: 0.6582 (m-80) cc_final: 0.6035 (m-80) REVERT: A 729 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4115 (m-10) REVERT: A 756 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.5724 (t80) REVERT: B 64 GLU cc_start: 0.8229 (tp30) cc_final: 0.8002 (tm-30) REVERT: B 138 GLU cc_start: 0.8132 (tp30) cc_final: 0.7925 (mt-10) REVERT: B 261 GLU cc_start: 0.8965 (mp0) cc_final: 0.8594 (mp0) REVERT: B 285 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: B 330 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8387 (mtpm) REVERT: B 339 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7548 (p) REVERT: B 351 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: B 367 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8085 (mmm-85) REVERT: B 379 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7771 (ttmm) REVERT: B 467 TYR cc_start: 0.9046 (p90) cc_final: 0.8806 (p90) REVERT: B 499 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 613 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (tt) REVERT: B 689 ILE cc_start: 0.5221 (OUTLIER) cc_final: 0.4729 (tp) REVERT: B 756 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.5137 (t80) REVERT: B 792 MET cc_start: 0.8740 (ttm) cc_final: 0.8169 (ttm) REVERT: C 47 GLU cc_start: 0.8191 (tp30) cc_final: 0.7878 (tt0) REVERT: C 57 TYR cc_start: 0.8059 (t80) cc_final: 0.7806 (t80) REVERT: C 58 ASP cc_start: 0.8434 (t0) cc_final: 0.8194 (t0) REVERT: C 83 LEU cc_start: 0.8667 (tp) cc_final: 0.8405 (tm) REVERT: C 152 ASP cc_start: 0.8224 (t0) cc_final: 0.7699 (t0) REVERT: C 208 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7751 (mt-10) REVERT: C 215 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 251 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7117 (mttp) REVERT: C 255 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6773 (mm-30) REVERT: C 338 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8573 (tppt) REVERT: C 467 TYR cc_start: 0.8714 (p90) cc_final: 0.7994 (p90) REVERT: C 499 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 551 ASP cc_start: 0.8880 (m-30) cc_final: 0.7991 (p0) REVERT: C 622 MET cc_start: 0.6120 (mtm) cc_final: 0.5880 (mtm) REVERT: C 670 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7451 (tm-30) REVERT: C 674 PHE cc_start: 0.6580 (m-80) cc_final: 0.6017 (m-80) REVERT: C 729 PHE cc_start: 0.4744 (OUTLIER) cc_final: 0.4148 (m-10) REVERT: C 738 ILE cc_start: 0.7833 (tp) cc_final: 0.7561 (pp) REVERT: D 64 GLU cc_start: 0.8273 (tp30) cc_final: 0.8055 (tm-30) REVERT: D 138 GLU cc_start: 0.8122 (tp30) cc_final: 0.7914 (mt-10) REVERT: D 261 GLU cc_start: 0.8965 (mp0) cc_final: 0.8580 (mp0) REVERT: D 285 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: D 330 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8359 (mtpm) REVERT: D 339 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7531 (p) REVERT: D 351 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: D 367 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8091 (mmm-85) REVERT: D 379 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7777 (ttmm) REVERT: D 467 TYR cc_start: 0.9045 (p90) cc_final: 0.8809 (p90) REVERT: D 499 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 613 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7638 (tt) REVERT: D 689 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4789 (tp) REVERT: D 756 TYR cc_start: 0.5362 (OUTLIER) cc_final: 0.5035 (t80) REVERT: D 792 MET cc_start: 0.8739 (ttm) cc_final: 0.8170 (ttm) outliers start: 82 outliers final: 14 residues processed: 372 average time/residue: 0.5541 time to fit residues: 240.5391 Evaluate side-chains 294 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 774 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 143 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN B 580 GLN C 30 GLN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN D 580 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086476 restraints weight = 38655.026| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.96 r_work: 0.3019 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25174 Z= 0.180 Angle : 0.562 9.890 34100 Z= 0.294 Chirality : 0.043 0.184 3898 Planarity : 0.003 0.029 4372 Dihedral : 4.878 59.189 3326 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.16 % Allowed : 13.07 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 3088 helix: 2.87 (0.16), residues: 1010 sheet: -0.01 (0.20), residues: 766 loop : -1.71 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 697 TYR 0.021 0.001 TYR C 115 PHE 0.015 0.001 PHE C 747 TRP 0.012 0.001 TRP D 662 HIS 0.003 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00417 (25174) covalent geometry : angle 0.56190 (34100) hydrogen bonds : bond 0.03926 ( 1224) hydrogen bonds : angle 4.67493 ( 3672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 278 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8218 (tp30) cc_final: 0.7838 (tt0) REVERT: A 57 TYR cc_start: 0.8113 (t80) cc_final: 0.7856 (t80) REVERT: A 58 ASP cc_start: 0.8504 (t0) cc_final: 0.8187 (t0) REVERT: A 83 LEU cc_start: 0.8650 (tp) cc_final: 0.8346 (tm) REVERT: A 152 ASP cc_start: 0.8174 (t0) cc_final: 0.7591 (t0) REVERT: A 208 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7761 (mt-10) REVERT: A 215 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 255 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: A 338 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8479 (tppt) REVERT: A 367 ARG cc_start: 0.8247 (tmt-80) cc_final: 0.7853 (mmm160) REVERT: A 467 TYR cc_start: 0.8699 (p90) cc_final: 0.7982 (p90) REVERT: A 551 ASP cc_start: 0.8817 (m-30) cc_final: 0.7932 (p0) REVERT: A 554 GLU cc_start: 0.8017 (mp0) cc_final: 0.7717 (tm-30) REVERT: A 622 MET cc_start: 0.6278 (mtm) cc_final: 0.5991 (mtm) REVERT: A 650 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.4975 (p90) REVERT: A 670 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 674 PHE cc_start: 0.6773 (m-80) cc_final: 0.6149 (m-80) REVERT: A 729 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.4280 (m-10) REVERT: A 756 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5689 (t80) REVERT: B 64 GLU cc_start: 0.8378 (tp30) cc_final: 0.7941 (tp30) REVERT: B 138 GLU cc_start: 0.8291 (tp30) cc_final: 0.8077 (mt-10) REVERT: B 261 GLU cc_start: 0.8845 (mp0) cc_final: 0.8498 (mp0) REVERT: B 330 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8425 (mtpm) REVERT: B 339 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 351 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: B 367 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8069 (mmm-85) REVERT: B 379 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7906 (ttmm) REVERT: B 467 TYR cc_start: 0.9042 (p90) cc_final: 0.8810 (p90) REVERT: B 499 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 613 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 683 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6785 (pp) REVERT: B 689 ILE cc_start: 0.5183 (OUTLIER) cc_final: 0.4632 (tp) REVERT: B 756 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.5169 (t80) REVERT: B 792 MET cc_start: 0.8642 (ttm) cc_final: 0.8289 (ttm) REVERT: C 47 GLU cc_start: 0.8217 (tp30) cc_final: 0.7839 (tt0) REVERT: C 57 TYR cc_start: 0.8109 (t80) cc_final: 0.7850 (t80) REVERT: C 58 ASP cc_start: 0.8483 (t0) cc_final: 0.8178 (t0) REVERT: C 83 LEU cc_start: 0.8672 (tp) cc_final: 0.8350 (tm) REVERT: C 152 ASP cc_start: 0.8118 (t0) cc_final: 0.7586 (t0) REVERT: C 208 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7763 (mt-10) REVERT: C 215 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 255 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: C 338 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8480 (tppt) REVERT: C 367 ARG cc_start: 0.8280 (tmt-80) cc_final: 0.7868 (mmm160) REVERT: C 467 TYR cc_start: 0.8715 (p90) cc_final: 0.8030 (p90) REVERT: C 528 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: C 551 ASP cc_start: 0.8842 (m-30) cc_final: 0.7937 (p0) REVERT: C 554 GLU cc_start: 0.8012 (mp0) cc_final: 0.7702 (tm-30) REVERT: C 622 MET cc_start: 0.6289 (mtm) cc_final: 0.6008 (mtm) REVERT: C 670 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 674 PHE cc_start: 0.6763 (m-80) cc_final: 0.6123 (m-80) REVERT: C 729 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4306 (m-10) REVERT: C 738 ILE cc_start: 0.7658 (tp) cc_final: 0.7413 (pp) REVERT: D 64 GLU cc_start: 0.8383 (tp30) cc_final: 0.7932 (tp30) REVERT: D 138 GLU cc_start: 0.8288 (tp30) cc_final: 0.8072 (mt-10) REVERT: D 261 GLU cc_start: 0.8946 (mp0) cc_final: 0.8540 (mp0) REVERT: D 285 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: D 330 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8417 (mtpm) REVERT: D 339 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7573 (p) REVERT: D 351 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: D 367 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8068 (mmm-85) REVERT: D 379 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7870 (ttmm) REVERT: D 467 TYR cc_start: 0.9039 (p90) cc_final: 0.8809 (p90) REVERT: D 499 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 613 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7757 (tt) REVERT: D 683 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6780 (pp) REVERT: D 689 ILE cc_start: 0.5233 (OUTLIER) cc_final: 0.4638 (tp) REVERT: D 756 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.5134 (t80) REVERT: D 792 MET cc_start: 0.8643 (ttm) cc_final: 0.8288 (ttm) outliers start: 88 outliers final: 22 residues processed: 348 average time/residue: 0.5598 time to fit residues: 227.8315 Evaluate side-chains 309 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 127 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 272 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 294 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN B 94 GLN B 155 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 223 ASN D 94 GLN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085321 restraints weight = 38579.942| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.95 r_work: 0.3065 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25174 Z= 0.199 Angle : 0.559 9.900 34100 Z= 0.291 Chirality : 0.043 0.163 3898 Planarity : 0.003 0.031 4372 Dihedral : 4.905 58.666 3322 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.55 % Rotamer: Outliers : 3.95 % Allowed : 14.18 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.16), residues: 3088 helix: 2.78 (0.16), residues: 1012 sheet: -0.12 (0.19), residues: 810 loop : -1.75 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.021 0.001 TYR A 115 PHE 0.018 0.001 PHE C 747 TRP 0.012 0.001 TRP C 546 HIS 0.004 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00464 (25174) covalent geometry : angle 0.55883 (34100) hydrogen bonds : bond 0.03927 ( 1224) hydrogen bonds : angle 4.66263 ( 3672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 268 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8243 (tp30) cc_final: 0.7901 (tt0) REVERT: A 57 TYR cc_start: 0.8156 (t80) cc_final: 0.7940 (t80) REVERT: A 58 ASP cc_start: 0.8541 (t0) cc_final: 0.8214 (t0) REVERT: A 83 LEU cc_start: 0.8717 (tp) cc_final: 0.8456 (tm) REVERT: A 152 ASP cc_start: 0.8152 (t0) cc_final: 0.7546 (t0) REVERT: A 208 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7837 (mt-10) REVERT: A 215 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 255 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 338 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8478 (tppt) REVERT: A 367 ARG cc_start: 0.8241 (tmt-80) cc_final: 0.7895 (mmm160) REVERT: A 395 LEU cc_start: 0.8535 (mt) cc_final: 0.8331 (mt) REVERT: A 467 TYR cc_start: 0.8764 (p90) cc_final: 0.8070 (p90) REVERT: A 551 ASP cc_start: 0.8839 (m-30) cc_final: 0.7885 (p0) REVERT: A 554 GLU cc_start: 0.8042 (mp0) cc_final: 0.7816 (tm-30) REVERT: A 622 MET cc_start: 0.6369 (mtm) cc_final: 0.6100 (mtm) REVERT: A 650 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.5271 (p90) REVERT: A 729 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4386 (m-10) REVERT: A 756 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5680 (t80) REVERT: B 30 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: B 64 GLU cc_start: 0.8414 (tp30) cc_final: 0.7950 (tp30) REVERT: B 261 GLU cc_start: 0.8933 (mp0) cc_final: 0.8570 (mp0) REVERT: B 330 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8436 (mtpm) REVERT: B 339 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7653 (p) REVERT: B 351 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: B 367 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.7940 (mmm-85) REVERT: B 379 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7978 (ttmm) REVERT: B 499 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 651 LEU cc_start: 0.8802 (tt) cc_final: 0.8594 (tm) REVERT: B 683 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6778 (pp) REVERT: B 689 ILE cc_start: 0.5139 (OUTLIER) cc_final: 0.4606 (tp) REVERT: B 756 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5224 (t80) REVERT: B 792 MET cc_start: 0.8744 (ttm) cc_final: 0.8317 (ttm) REVERT: C 47 GLU cc_start: 0.8244 (tp30) cc_final: 0.7902 (tt0) REVERT: C 57 TYR cc_start: 0.8157 (t80) cc_final: 0.7941 (t80) REVERT: C 58 ASP cc_start: 0.8547 (t0) cc_final: 0.8210 (t0) REVERT: C 83 LEU cc_start: 0.8702 (tp) cc_final: 0.8438 (tm) REVERT: C 152 ASP cc_start: 0.8213 (t0) cc_final: 0.7656 (t0) REVERT: C 208 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7878 (mt-10) REVERT: C 215 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 255 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: C 338 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8479 (tppt) REVERT: C 467 TYR cc_start: 0.8771 (p90) cc_final: 0.8066 (p90) REVERT: C 551 ASP cc_start: 0.8846 (m-30) cc_final: 0.7897 (p0) REVERT: C 554 GLU cc_start: 0.8051 (mp0) cc_final: 0.7815 (tm-30) REVERT: C 622 MET cc_start: 0.6340 (mtm) cc_final: 0.6079 (mtm) REVERT: C 650 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5428 (p90) REVERT: C 670 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 30 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: D 64 GLU cc_start: 0.8418 (tp30) cc_final: 0.7952 (tp30) REVERT: D 247 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7064 (mtp85) REVERT: D 261 GLU cc_start: 0.8950 (mp0) cc_final: 0.8581 (mp0) REVERT: D 285 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: D 330 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8434 (mtpm) REVERT: D 339 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7647 (p) REVERT: D 351 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: D 367 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7926 (mmm-85) REVERT: D 379 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7979 (ttmm) REVERT: D 499 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7724 (mt-10) REVERT: D 613 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7875 (tt) REVERT: D 638 VAL cc_start: 0.8767 (p) cc_final: 0.8566 (m) REVERT: D 683 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6780 (pp) REVERT: D 689 ILE cc_start: 0.5134 (OUTLIER) cc_final: 0.4602 (tp) REVERT: D 756 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.5231 (t80) REVERT: D 792 MET cc_start: 0.8745 (ttm) cc_final: 0.8319 (ttm) outliers start: 110 outliers final: 42 residues processed: 350 average time/residue: 0.5694 time to fit residues: 233.6858 Evaluate side-chains 310 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 300 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN B 155 ASN B 541 ASN ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 113 HIS C 223 ASN C 724 ASN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084205 restraints weight = 38779.198| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.95 r_work: 0.3034 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25174 Z= 0.224 Angle : 0.576 10.452 34100 Z= 0.299 Chirality : 0.043 0.166 3898 Planarity : 0.003 0.031 4372 Dihedral : 5.011 57.706 3322 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.64 % Favored : 92.29 % Rotamer: Outliers : 4.27 % Allowed : 14.39 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 3088 helix: 2.68 (0.15), residues: 1012 sheet: -0.13 (0.19), residues: 816 loop : -1.76 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 193 TYR 0.021 0.001 TYR A 115 PHE 0.018 0.001 PHE C 747 TRP 0.013 0.001 TRP C 546 HIS 0.006 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00525 (25174) covalent geometry : angle 0.57625 (34100) hydrogen bonds : bond 0.04015 ( 1224) hydrogen bonds : angle 4.70223 ( 3672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 261 time to evaluate : 1.083 Fit side-chains REVERT: A 57 TYR cc_start: 0.8184 (t80) cc_final: 0.7975 (t80) REVERT: A 58 ASP cc_start: 0.8524 (t0) cc_final: 0.8166 (t0) REVERT: A 83 LEU cc_start: 0.8711 (tp) cc_final: 0.8385 (tm) REVERT: A 152 ASP cc_start: 0.8158 (t0) cc_final: 0.7558 (t0) REVERT: A 208 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7884 (mt-10) REVERT: A 215 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 255 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: A 338 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8384 (tppt) REVERT: A 367 ARG cc_start: 0.8320 (tmt-80) cc_final: 0.7895 (mmm160) REVERT: A 467 TYR cc_start: 0.8703 (p90) cc_final: 0.7987 (p90) REVERT: A 551 ASP cc_start: 0.8793 (m-30) cc_final: 0.7857 (p0) REVERT: A 554 GLU cc_start: 0.7988 (mp0) cc_final: 0.7741 (tm-30) REVERT: A 622 MET cc_start: 0.6355 (mtm) cc_final: 0.6074 (mtm) REVERT: A 650 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.5224 (p90) REVERT: A 756 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5672 (t80) REVERT: B 30 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: B 64 GLU cc_start: 0.8453 (tp30) cc_final: 0.8002 (tp30) REVERT: B 255 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7475 (mp0) REVERT: B 261 GLU cc_start: 0.8868 (mp0) cc_final: 0.8517 (mp0) REVERT: B 330 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8440 (mtpm) REVERT: B 351 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: B 367 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.7920 (mmm-85) REVERT: B 379 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7895 (ttmm) REVERT: B 499 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 683 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6850 (pt) REVERT: B 689 ILE cc_start: 0.5123 (OUTLIER) cc_final: 0.4603 (tp) REVERT: B 756 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.5270 (t80) REVERT: B 792 MET cc_start: 0.8799 (ttm) cc_final: 0.8440 (ttm) REVERT: C 57 TYR cc_start: 0.8187 (t80) cc_final: 0.7978 (t80) REVERT: C 58 ASP cc_start: 0.8547 (t0) cc_final: 0.8185 (t0) REVERT: C 83 LEU cc_start: 0.8707 (tp) cc_final: 0.8380 (tm) REVERT: C 152 ASP cc_start: 0.8182 (t0) cc_final: 0.7535 (t0) REVERT: C 208 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7884 (mt-10) REVERT: C 215 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7794 (mm-30) REVERT: C 255 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: C 338 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8383 (tppt) REVERT: C 367 ARG cc_start: 0.8283 (tpm-80) cc_final: 0.7876 (mmm160) REVERT: C 467 TYR cc_start: 0.8706 (p90) cc_final: 0.7998 (p90) REVERT: C 551 ASP cc_start: 0.8801 (m-30) cc_final: 0.7864 (p0) REVERT: C 554 GLU cc_start: 0.7986 (mp0) cc_final: 0.7732 (tm-30) REVERT: C 622 MET cc_start: 0.6341 (mtm) cc_final: 0.6029 (mtm) REVERT: C 650 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5434 (p90) REVERT: D 30 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: D 64 GLU cc_start: 0.8457 (tp30) cc_final: 0.8006 (tp30) REVERT: D 247 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7034 (mtp85) REVERT: D 255 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7449 (mp0) REVERT: D 261 GLU cc_start: 0.8919 (mp0) cc_final: 0.8546 (mp0) REVERT: D 285 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: D 330 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8369 (mtpm) REVERT: D 351 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: D 367 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7893 (mmm-85) REVERT: D 379 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7886 (ttmm) REVERT: D 499 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D 683 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6839 (pt) REVERT: D 689 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4600 (tp) REVERT: D 756 TYR cc_start: 0.5509 (OUTLIER) cc_final: 0.5277 (t80) REVERT: D 792 MET cc_start: 0.8782 (ttm) cc_final: 0.8424 (ttm) outliers start: 119 outliers final: 46 residues processed: 352 average time/residue: 0.5872 time to fit residues: 242.7002 Evaluate side-chains 302 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 264 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 246 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN A 283 GLN B 94 GLN B 155 ASN ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 113 HIS C 223 ASN C 283 GLN D 94 GLN D 155 ASN D 541 ASN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.141740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087001 restraints weight = 38459.239| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.95 r_work: 0.3078 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25174 Z= 0.135 Angle : 0.538 9.534 34100 Z= 0.279 Chirality : 0.041 0.162 3898 Planarity : 0.003 0.030 4372 Dihedral : 4.895 59.691 3322 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.58 % Rotamer: Outliers : 3.19 % Allowed : 15.90 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 3088 helix: 2.88 (0.16), residues: 1012 sheet: -0.07 (0.20), residues: 808 loop : -1.72 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 193 TYR 0.023 0.001 TYR C 115 PHE 0.018 0.001 PHE C 747 TRP 0.010 0.001 TRP C 546 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00309 (25174) covalent geometry : angle 0.53837 (34100) hydrogen bonds : bond 0.03603 ( 1224) hydrogen bonds : angle 4.52602 ( 3672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 266 time to evaluate : 0.986 Fit side-chains REVERT: A 47 GLU cc_start: 0.8192 (tp30) cc_final: 0.7908 (tt0) REVERT: A 57 TYR cc_start: 0.8183 (t80) cc_final: 0.7982 (t80) REVERT: A 58 ASP cc_start: 0.8533 (t0) cc_final: 0.8189 (t0) REVERT: A 83 LEU cc_start: 0.8753 (tp) cc_final: 0.8462 (tm) REVERT: A 152 ASP cc_start: 0.8161 (t0) cc_final: 0.7548 (t0) REVERT: A 205 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 208 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7834 (mt-10) REVERT: A 215 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 255 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: A 338 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8491 (tppt) REVERT: A 367 ARG cc_start: 0.8294 (tmt-80) cc_final: 0.7932 (mmm160) REVERT: A 467 TYR cc_start: 0.8752 (p90) cc_final: 0.8060 (p90) REVERT: A 551 ASP cc_start: 0.8815 (m-30) cc_final: 0.7877 (p0) REVERT: A 554 GLU cc_start: 0.8029 (mp0) cc_final: 0.7776 (tm-30) REVERT: A 622 MET cc_start: 0.6414 (mtm) cc_final: 0.6162 (mtm) REVERT: A 650 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5035 (p90) REVERT: A 756 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5585 (t80) REVERT: B 30 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: B 64 GLU cc_start: 0.8426 (tp30) cc_final: 0.7957 (tp30) REVERT: B 261 GLU cc_start: 0.8888 (mp0) cc_final: 0.8568 (mp0) REVERT: B 285 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7940 (mtpt) REVERT: B 330 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8445 (mtpm) REVERT: B 339 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7658 (p) REVERT: B 351 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: B 367 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7914 (mmm-85) REVERT: B 379 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7917 (ttmm) REVERT: B 499 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7754 (mt-10) REVERT: B 689 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4658 (tp) REVERT: B 756 TYR cc_start: 0.5607 (OUTLIER) cc_final: 0.5303 (t80) REVERT: B 792 MET cc_start: 0.8774 (ttm) cc_final: 0.8321 (ttm) REVERT: C 47 GLU cc_start: 0.8189 (tp30) cc_final: 0.7907 (tt0) REVERT: C 58 ASP cc_start: 0.8534 (t0) cc_final: 0.8191 (t0) REVERT: C 83 LEU cc_start: 0.8743 (tp) cc_final: 0.8454 (tm) REVERT: C 152 ASP cc_start: 0.8086 (t0) cc_final: 0.7494 (t0) REVERT: C 205 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7549 (p0) REVERT: C 208 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7836 (mt-10) REVERT: C 215 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 255 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: C 338 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8486 (tppt) REVERT: C 367 ARG cc_start: 0.8201 (tpm-80) cc_final: 0.7680 (tpp-160) REVERT: C 467 TYR cc_start: 0.8753 (p90) cc_final: 0.8056 (p90) REVERT: C 528 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8553 (tp30) REVERT: C 551 ASP cc_start: 0.8805 (m-30) cc_final: 0.7913 (p0) REVERT: C 554 GLU cc_start: 0.8029 (mp0) cc_final: 0.7773 (tm-30) REVERT: C 622 MET cc_start: 0.6403 (mtm) cc_final: 0.6156 (mtm) REVERT: C 650 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5340 (p90) REVERT: C 670 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7078 (tm-30) REVERT: D 30 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: D 64 GLU cc_start: 0.8417 (tp30) cc_final: 0.7952 (tp30) REVERT: D 247 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7002 (mtp85) REVERT: D 261 GLU cc_start: 0.8948 (mp0) cc_final: 0.8629 (mp0) REVERT: D 285 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8070 (mtpt) REVERT: D 330 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8443 (mtpm) REVERT: D 339 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7654 (p) REVERT: D 367 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7942 (mmm-85) REVERT: D 379 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7919 (ttmm) REVERT: D 499 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 689 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4655 (tp) REVERT: D 756 TYR cc_start: 0.5517 (OUTLIER) cc_final: 0.5243 (t80) REVERT: D 792 MET cc_start: 0.8758 (ttm) cc_final: 0.8297 (ttm) outliers start: 89 outliers final: 35 residues processed: 332 average time/residue: 0.5821 time to fit residues: 226.3140 Evaluate side-chains 303 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 211 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN A 283 GLN B 155 ASN ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 113 HIS C 223 ASN C 283 GLN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085643 restraints weight = 38520.479| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.95 r_work: 0.3064 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25174 Z= 0.170 Angle : 0.573 10.132 34100 Z= 0.295 Chirality : 0.042 0.168 3898 Planarity : 0.003 0.033 4372 Dihedral : 4.899 56.982 3322 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 3.27 % Allowed : 16.87 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 3088 helix: 2.81 (0.15), residues: 1012 sheet: -0.09 (0.20), residues: 796 loop : -1.62 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.023 0.001 TYR C 115 PHE 0.016 0.001 PHE C 747 TRP 0.011 0.001 TRP C 546 HIS 0.004 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00397 (25174) covalent geometry : angle 0.57299 (34100) hydrogen bonds : bond 0.03778 ( 1224) hydrogen bonds : angle 4.54859 ( 3672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 250 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8232 (tp30) cc_final: 0.7898 (tt0) REVERT: A 57 TYR cc_start: 0.8169 (t80) cc_final: 0.7952 (t80) REVERT: A 58 ASP cc_start: 0.8564 (t0) cc_final: 0.8212 (t0) REVERT: A 83 LEU cc_start: 0.8756 (tp) cc_final: 0.8460 (tm) REVERT: A 152 ASP cc_start: 0.8159 (t0) cc_final: 0.7552 (t0) REVERT: A 205 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 208 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7842 (mt-10) REVERT: A 215 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 255 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: A 338 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8417 (tppt) REVERT: A 367 ARG cc_start: 0.8313 (tmt-80) cc_final: 0.8037 (mmm160) REVERT: A 467 TYR cc_start: 0.8758 (p90) cc_final: 0.8090 (p90) REVERT: A 551 ASP cc_start: 0.8761 (m-30) cc_final: 0.7801 (p0) REVERT: A 553 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6612 (pp) REVERT: A 622 MET cc_start: 0.6380 (mtm) cc_final: 0.6140 (mtm) REVERT: A 650 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.5152 (p90) REVERT: A 672 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8131 (ttmm) REVERT: A 756 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5587 (t80) REVERT: B 30 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: B 64 GLU cc_start: 0.8437 (tp30) cc_final: 0.7968 (tp30) REVERT: B 255 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7547 (mp0) REVERT: B 261 GLU cc_start: 0.8894 (mp0) cc_final: 0.8569 (mp0) REVERT: B 285 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8027 (mtpt) REVERT: B 330 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8464 (mtpm) REVERT: B 339 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (p) REVERT: B 351 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: B 379 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7940 (ttmm) REVERT: B 499 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 689 ILE cc_start: 0.5272 (OUTLIER) cc_final: 0.4793 (tp) REVERT: B 756 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.5269 (t80) REVERT: B 792 MET cc_start: 0.8771 (ttm) cc_final: 0.8295 (ttm) REVERT: C 47 GLU cc_start: 0.8227 (tp30) cc_final: 0.7896 (tt0) REVERT: C 58 ASP cc_start: 0.8522 (t0) cc_final: 0.8183 (t0) REVERT: C 83 LEU cc_start: 0.8752 (tp) cc_final: 0.8435 (tm) REVERT: C 152 ASP cc_start: 0.8105 (t0) cc_final: 0.7461 (t0) REVERT: C 205 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7567 (p0) REVERT: C 208 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7844 (mt-10) REVERT: C 215 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7795 (mm-30) REVERT: C 255 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: C 338 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8474 (tppt) REVERT: C 367 ARG cc_start: 0.8182 (tpm-80) cc_final: 0.7764 (tpp-160) REVERT: C 467 TYR cc_start: 0.8761 (p90) cc_final: 0.8091 (p90) REVERT: C 528 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8567 (tp30) REVERT: C 551 ASP cc_start: 0.8807 (m-30) cc_final: 0.7912 (p0) REVERT: C 554 GLU cc_start: 0.8044 (mp0) cc_final: 0.7818 (tm-30) REVERT: C 622 MET cc_start: 0.6371 (mtm) cc_final: 0.6122 (mtm) REVERT: C 650 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.5358 (p90) REVERT: C 670 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7109 (tm-30) REVERT: D 30 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: D 64 GLU cc_start: 0.8426 (tp30) cc_final: 0.7956 (tp30) REVERT: D 247 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6986 (mtp85) REVERT: D 255 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7524 (mp0) REVERT: D 261 GLU cc_start: 0.8960 (mp0) cc_final: 0.8659 (mp0) REVERT: D 285 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: D 330 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8458 (mtpm) REVERT: D 339 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7684 (p) REVERT: D 351 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: D 379 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7939 (ttmm) REVERT: D 499 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7801 (mt-10) REVERT: D 689 ILE cc_start: 0.5358 (OUTLIER) cc_final: 0.4836 (tp) REVERT: D 756 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.5273 (t80) REVERT: D 792 MET cc_start: 0.8762 (ttm) cc_final: 0.8280 (ttm) outliers start: 91 outliers final: 42 residues processed: 321 average time/residue: 0.5768 time to fit residues: 216.4794 Evaluate side-chains 305 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 210 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN A 283 GLN B 155 ASN ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 113 HIS C 223 ASN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085251 restraints weight = 38668.423| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.94 r_work: 0.3053 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25174 Z= 0.194 Angle : 0.590 11.498 34100 Z= 0.302 Chirality : 0.043 0.180 3898 Planarity : 0.003 0.032 4372 Dihedral : 4.956 57.265 3322 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.34 % Allowed : 17.12 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.16), residues: 3088 helix: 2.75 (0.15), residues: 1010 sheet: -0.15 (0.19), residues: 800 loop : -1.62 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.022 0.001 TYR C 115 PHE 0.015 0.001 PHE C 747 TRP 0.012 0.001 TRP C 546 HIS 0.003 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00456 (25174) covalent geometry : angle 0.59005 (34100) hydrogen bonds : bond 0.03883 ( 1224) hydrogen bonds : angle 4.59192 ( 3672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 248 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8273 (tp30) cc_final: 0.7949 (tt0) REVERT: A 57 TYR cc_start: 0.8174 (t80) cc_final: 0.7954 (t80) REVERT: A 58 ASP cc_start: 0.8565 (t0) cc_final: 0.8197 (t0) REVERT: A 83 LEU cc_start: 0.8761 (tp) cc_final: 0.8438 (tm) REVERT: A 152 ASP cc_start: 0.8147 (t0) cc_final: 0.7499 (t0) REVERT: A 205 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 208 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7889 (mt-10) REVERT: A 215 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 255 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: A 338 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8424 (tppt) REVERT: A 367 ARG cc_start: 0.8336 (tmt-80) cc_final: 0.8049 (mmm160) REVERT: A 467 TYR cc_start: 0.8765 (p90) cc_final: 0.8096 (p90) REVERT: A 551 ASP cc_start: 0.8767 (m-30) cc_final: 0.7797 (p0) REVERT: A 622 MET cc_start: 0.6396 (mtm) cc_final: 0.6130 (mtm) REVERT: A 650 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5108 (p90) REVERT: A 756 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5545 (t80) REVERT: B 30 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 64 GLU cc_start: 0.8473 (tp30) cc_final: 0.7998 (tp30) REVERT: B 255 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7505 (mp0) REVERT: B 261 GLU cc_start: 0.8914 (mp0) cc_final: 0.8600 (mp0) REVERT: B 330 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8450 (mtpm) REVERT: B 339 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7643 (p) REVERT: B 351 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: B 367 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7831 (ptp-110) REVERT: B 379 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7933 (ttmm) REVERT: B 499 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 683 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6785 (pt) REVERT: B 689 ILE cc_start: 0.5238 (OUTLIER) cc_final: 0.4762 (tp) REVERT: B 756 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.5178 (t80) REVERT: B 792 MET cc_start: 0.8821 (ttm) cc_final: 0.8399 (ttm) REVERT: C 47 GLU cc_start: 0.8268 (tp30) cc_final: 0.7960 (tt0) REVERT: C 58 ASP cc_start: 0.8531 (t0) cc_final: 0.8195 (t0) REVERT: C 83 LEU cc_start: 0.8754 (tp) cc_final: 0.8426 (tm) REVERT: C 152 ASP cc_start: 0.8133 (t0) cc_final: 0.7488 (t0) REVERT: C 205 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (p0) REVERT: C 208 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 215 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 255 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: C 338 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8411 (tppt) REVERT: C 367 ARG cc_start: 0.8188 (tpm-80) cc_final: 0.7780 (tpp-160) REVERT: C 467 TYR cc_start: 0.8763 (p90) cc_final: 0.8094 (p90) REVERT: C 528 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8576 (tp30) REVERT: C 551 ASP cc_start: 0.8817 (m-30) cc_final: 0.7901 (p0) REVERT: C 622 MET cc_start: 0.6360 (mtm) cc_final: 0.6097 (mtm) REVERT: C 650 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.5373 (p90) REVERT: C 670 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 30 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: D 64 GLU cc_start: 0.8450 (tp30) cc_final: 0.7976 (tp30) REVERT: D 247 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6996 (mtp85) REVERT: D 255 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7508 (mp0) REVERT: D 261 GLU cc_start: 0.8966 (mp0) cc_final: 0.8569 (mp0) REVERT: D 285 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8247 (mtpp) REVERT: D 330 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8448 (mtpm) REVERT: D 339 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7678 (p) REVERT: D 351 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: D 367 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7825 (ptp-110) REVERT: D 379 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7928 (ttmm) REVERT: D 499 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 683 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6795 (pt) REVERT: D 689 ILE cc_start: 0.5358 (OUTLIER) cc_final: 0.4848 (tp) REVERT: D 756 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.5179 (t80) REVERT: D 792 MET cc_start: 0.8788 (ttm) cc_final: 0.8434 (ttm) outliers start: 93 outliers final: 51 residues processed: 323 average time/residue: 0.5528 time to fit residues: 209.9362 Evaluate side-chains 317 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 240 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 223 ASN B 155 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS C 223 ASN C 283 GLN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087197 restraints weight = 38466.262| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.94 r_work: 0.3081 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25174 Z= 0.133 Angle : 0.562 9.939 34100 Z= 0.289 Chirality : 0.042 0.168 3898 Planarity : 0.003 0.030 4372 Dihedral : 4.883 57.877 3322 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 2.69 % Allowed : 18.16 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.16), residues: 3088 helix: 2.87 (0.15), residues: 1014 sheet: -0.06 (0.20), residues: 788 loop : -1.63 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.025 0.001 TYR A 115 PHE 0.015 0.001 PHE C 747 TRP 0.010 0.001 TRP C 546 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00305 (25174) covalent geometry : angle 0.56212 (34100) hydrogen bonds : bond 0.03614 ( 1224) hydrogen bonds : angle 4.47969 ( 3672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8245 (tp30) cc_final: 0.7911 (tt0) REVERT: A 57 TYR cc_start: 0.8176 (t80) cc_final: 0.7972 (t80) REVERT: A 58 ASP cc_start: 0.8540 (t0) cc_final: 0.8186 (t0) REVERT: A 83 LEU cc_start: 0.8751 (tp) cc_final: 0.8460 (tm) REVERT: A 152 ASP cc_start: 0.8152 (t0) cc_final: 0.7505 (t0) REVERT: A 205 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (p0) REVERT: A 208 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7820 (mt-10) REVERT: A 215 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 255 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: A 338 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8442 (tppt) REVERT: A 367 ARG cc_start: 0.8282 (tmt-80) cc_final: 0.7960 (tpp-160) REVERT: A 467 TYR cc_start: 0.8741 (p90) cc_final: 0.8060 (p90) REVERT: A 551 ASP cc_start: 0.8767 (m-30) cc_final: 0.7779 (p0) REVERT: A 622 MET cc_start: 0.6416 (mtm) cc_final: 0.6106 (mtm) REVERT: A 650 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5104 (p90) REVERT: A 662 TRP cc_start: 0.7820 (m100) cc_final: 0.7532 (m100) REVERT: A 672 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8084 (ttmm) REVERT: A 756 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5516 (t80) REVERT: B 30 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: B 64 GLU cc_start: 0.8414 (tp30) cc_final: 0.7946 (tp30) REVERT: B 189 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 255 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7497 (mp0) REVERT: B 261 GLU cc_start: 0.8930 (mp0) cc_final: 0.8638 (mp0) REVERT: B 285 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7945 (mtpt) REVERT: B 330 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8446 (mtpm) REVERT: B 339 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7679 (p) REVERT: B 379 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7910 (ttmm) REVERT: B 499 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 689 ILE cc_start: 0.5255 (OUTLIER) cc_final: 0.4787 (tp) REVERT: B 756 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.5042 (t80) REVERT: B 792 MET cc_start: 0.8823 (ttm) cc_final: 0.8313 (ttm) REVERT: C 47 GLU cc_start: 0.8265 (tp30) cc_final: 0.7905 (tt0) REVERT: C 58 ASP cc_start: 0.8499 (t0) cc_final: 0.8162 (t0) REVERT: C 83 LEU cc_start: 0.8738 (tp) cc_final: 0.8445 (tm) REVERT: C 152 ASP cc_start: 0.8118 (t0) cc_final: 0.7483 (t0) REVERT: C 205 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7554 (p0) REVERT: C 208 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7825 (mt-10) REVERT: C 215 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 255 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: C 338 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8470 (tppt) REVERT: C 367 ARG cc_start: 0.8134 (tpm-80) cc_final: 0.7726 (tpp-160) REVERT: C 467 TYR cc_start: 0.8732 (p90) cc_final: 0.8053 (p90) REVERT: C 528 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: C 551 ASP cc_start: 0.8762 (m-30) cc_final: 0.7815 (p0) REVERT: C 622 MET cc_start: 0.6378 (mtm) cc_final: 0.6054 (mtm) REVERT: C 650 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.5344 (p90) REVERT: C 662 TRP cc_start: 0.7862 (m100) cc_final: 0.7513 (m100) REVERT: C 670 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6990 (tm-30) REVERT: C 672 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7958 (ttmm) REVERT: D 30 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: D 64 GLU cc_start: 0.8411 (tp30) cc_final: 0.7944 (tp30) REVERT: D 247 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6964 (mtp85) REVERT: D 255 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7482 (mp0) REVERT: D 261 GLU cc_start: 0.8981 (mp0) cc_final: 0.8599 (mp0) REVERT: D 285 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (mtpp) REVERT: D 330 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8445 (mtpm) REVERT: D 339 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (p) REVERT: D 351 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: D 367 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7880 (ptp-110) REVERT: D 379 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7913 (ttmm) REVERT: D 499 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 683 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6722 (pt) REVERT: D 689 ILE cc_start: 0.5216 (OUTLIER) cc_final: 0.4721 (tp) REVERT: D 756 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.5037 (t80) REVERT: D 792 MET cc_start: 0.8775 (ttm) cc_final: 0.8336 (ttm) outliers start: 75 outliers final: 40 residues processed: 312 average time/residue: 0.5303 time to fit residues: 193.1927 Evaluate side-chains 308 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 286 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 251 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 113 HIS A 223 ASN A 283 GLN B 155 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS C 30 GLN C 113 HIS C 223 ASN C 283 GLN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086489 restraints weight = 38623.137| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.95 r_work: 0.3066 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25174 Z= 0.161 Angle : 0.574 10.745 34100 Z= 0.295 Chirality : 0.042 0.168 3898 Planarity : 0.003 0.031 4372 Dihedral : 4.896 57.025 3322 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 2.84 % Allowed : 18.20 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 3088 helix: 2.83 (0.15), residues: 1014 sheet: -0.06 (0.20), residues: 790 loop : -1.63 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 193 TYR 0.025 0.001 TYR A 115 PHE 0.015 0.001 PHE C 747 TRP 0.011 0.001 TRP C 546 HIS 0.005 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00376 (25174) covalent geometry : angle 0.57425 (34100) hydrogen bonds : bond 0.03726 ( 1224) hydrogen bonds : angle 4.52010 ( 3672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 253 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8281 (tp30) cc_final: 0.7943 (tt0) REVERT: A 57 TYR cc_start: 0.8154 (t80) cc_final: 0.7937 (t80) REVERT: A 58 ASP cc_start: 0.8563 (t0) cc_final: 0.8213 (t0) REVERT: A 83 LEU cc_start: 0.8758 (tp) cc_final: 0.8435 (tm) REVERT: A 152 ASP cc_start: 0.8134 (t0) cc_final: 0.7545 (t0) REVERT: A 205 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 208 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7837 (mt-10) REVERT: A 215 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 255 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6768 (mm-30) REVERT: A 338 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8435 (tppt) REVERT: A 367 ARG cc_start: 0.8280 (tmt-80) cc_final: 0.8018 (mmm160) REVERT: A 467 TYR cc_start: 0.8742 (p90) cc_final: 0.8068 (p90) REVERT: A 551 ASP cc_start: 0.8770 (m-30) cc_final: 0.7787 (p0) REVERT: A 622 MET cc_start: 0.6395 (mtm) cc_final: 0.6083 (mtm) REVERT: A 650 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5092 (p90) REVERT: A 651 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7998 (tm) REVERT: A 662 TRP cc_start: 0.7867 (m100) cc_final: 0.7575 (m100) REVERT: A 672 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8044 (ttmm) REVERT: A 756 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.5446 (t80) REVERT: B 30 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: B 64 GLU cc_start: 0.8429 (tp30) cc_final: 0.7961 (tp30) REVERT: B 111 MET cc_start: 0.8066 (tpp) cc_final: 0.7754 (tpt) REVERT: B 255 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7476 (mp0) REVERT: B 261 GLU cc_start: 0.8901 (mp0) cc_final: 0.8574 (mp0) REVERT: B 285 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8007 (mtpt) REVERT: B 330 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8465 (mtpm) REVERT: B 339 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7618 (p) REVERT: B 351 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: B 379 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7924 (ttmm) REVERT: B 499 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 689 ILE cc_start: 0.5155 (OUTLIER) cc_final: 0.4698 (tp) REVERT: B 756 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.5022 (t80) REVERT: B 792 MET cc_start: 0.8842 (ttm) cc_final: 0.8348 (ttm) REVERT: C 47 GLU cc_start: 0.8286 (tp30) cc_final: 0.7949 (tt0) REVERT: C 58 ASP cc_start: 0.8520 (t0) cc_final: 0.8195 (t0) REVERT: C 83 LEU cc_start: 0.8747 (tp) cc_final: 0.8424 (tm) REVERT: C 152 ASP cc_start: 0.8111 (t0) cc_final: 0.7475 (t0) REVERT: C 205 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7560 (p0) REVERT: C 208 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7828 (mt-10) REVERT: C 215 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7782 (mm-30) REVERT: C 255 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: C 338 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8479 (tppt) REVERT: C 367 ARG cc_start: 0.8153 (tpm-80) cc_final: 0.7752 (tpp-160) REVERT: C 467 TYR cc_start: 0.8736 (p90) cc_final: 0.8062 (p90) REVERT: C 528 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8554 (tp30) REVERT: C 551 ASP cc_start: 0.8744 (m-30) cc_final: 0.7801 (p0) REVERT: C 622 MET cc_start: 0.6368 (mtm) cc_final: 0.6040 (mtm) REVERT: C 650 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.5288 (p90) REVERT: C 651 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7963 (tm) REVERT: C 662 TRP cc_start: 0.7871 (m100) cc_final: 0.7521 (m100) REVERT: C 670 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6930 (tm-30) REVERT: C 672 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7863 (ttmm) REVERT: C 729 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.4804 (m-10) REVERT: D 30 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: D 64 GLU cc_start: 0.8425 (tp30) cc_final: 0.7957 (tp30) REVERT: D 247 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6963 (mtp85) REVERT: D 255 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7477 (mp0) REVERT: D 261 GLU cc_start: 0.8975 (mp0) cc_final: 0.8574 (mp0) REVERT: D 285 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: D 330 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8452 (mtpm) REVERT: D 339 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7625 (p) REVERT: D 351 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: D 379 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7922 (ttmm) REVERT: D 499 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 683 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6721 (pt) REVERT: D 689 ILE cc_start: 0.5148 (OUTLIER) cc_final: 0.4691 (tp) REVERT: D 756 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.5020 (t80) REVERT: D 792 MET cc_start: 0.8849 (ttm) cc_final: 0.8423 (ttm) outliers start: 79 outliers final: 45 residues processed: 315 average time/residue: 0.6189 time to fit residues: 227.0784 Evaluate side-chains 318 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 667 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 756 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 168 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 283 optimal weight: 0.2980 chunk 266 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 178 optimal weight: 0.0170 chunk 140 optimal weight: 7.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 223 ASN A 283 GLN B 155 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS C 223 ASN C 283 GLN D 155 ASN ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086612 restraints weight = 38471.914| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.95 r_work: 0.3074 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 25174 Z= 0.266 Angle : 1.036 59.109 34100 Z= 0.647 Chirality : 0.046 0.771 3898 Planarity : 0.004 0.110 4372 Dihedral : 4.970 57.063 3322 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 2.80 % Allowed : 18.31 % Favored : 78.89 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 3088 helix: 2.82 (0.15), residues: 1014 sheet: -0.08 (0.20), residues: 790 loop : -1.63 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.024 0.001 TYR A 115 PHE 0.014 0.001 PHE C 747 TRP 0.011 0.001 TRP C 546 HIS 0.167 0.008 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00452 (25174) covalent geometry : angle 1.03551 (34100) hydrogen bonds : bond 0.03730 ( 1224) hydrogen bonds : angle 4.52883 ( 3672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10615.22 seconds wall clock time: 181 minutes 14.89 seconds (10874.89 seconds total)