Starting phenix.real_space_refine on Sat Aug 8 12:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjp_65118/08_2026/9vjp_65118.map" } resolution = 3.29 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= 0.001 sd= 0.008 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 116 5.16 5 C 17988 2.51 5 N 4500 2.21 5 O 4952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27572 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6845 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 16 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6845 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 16 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6845 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 16 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6845 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 16 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.95, per 1000 atoms: 0.18 Number of scatterers: 27572 At special positions: 0 Unit cell: (124.168, 124.168, 147.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 116 16.00 P 12 15.00 O 4952 8.00 N 4500 7.00 C 17988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 930.0 milliseconds 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 77.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.081A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.846A pdb=" N LEU A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.611A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.516A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.951A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 454 through 468 removed outlier: 5.032A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.819A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 removed outlier: 3.737A pdb=" N THR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.705A pdb=" N THR A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.731A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.765A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 removed outlier: 3.558A pdb=" N GLU A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.516A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 788 removed outlier: 4.045A pdb=" N MET A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 796 through 818 Processing helix chain 'A' and resid 821 through 843 removed outlier: 3.685A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 Processing helix chain 'A' and resid 853 through 890 removed outlier: 4.326A pdb=" N PHE A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 913 removed outlier: 3.708A pdb=" N ILE A 899 " --> pdb=" O ARG A 895 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 957 through 987 Processing helix chain 'A' and resid 990 through 1008 removed outlier: 4.291A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1023 removed outlier: 3.569A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1069 removed outlier: 3.668A pdb=" N THR A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1074 removed outlier: 4.068A pdb=" N ASP A1073 " --> pdb=" O LYS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1104 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 201 removed outlier: 4.098A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.847A pdb=" N LEU B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.536A pdb=" N VAL B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.545A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.962A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 454 through 468 removed outlier: 5.043A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.825A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 removed outlier: 3.770A pdb=" N THR B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.709A pdb=" N THR B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.718A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.763A pdb=" N ALA B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.555A pdb=" N GLU B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 665 through 671 removed outlier: 3.503A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 788 removed outlier: 4.052A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 795 Processing helix chain 'B' and resid 796 through 818 Processing helix chain 'B' and resid 821 through 843 removed outlier: 3.660A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 849 Processing helix chain 'B' and resid 853 through 890 removed outlier: 4.360A pdb=" N PHE B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 913 removed outlier: 3.716A pdb=" N ILE B 899 " --> pdb=" O ARG B 895 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 957 through 987 Processing helix chain 'B' and resid 990 through 1008 removed outlier: 4.307A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1023 removed outlier: 3.590A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1069 removed outlier: 3.661A pdb=" N THR B1069 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1074 removed outlier: 4.092A pdb=" N ASP B1073 " --> pdb=" O LYS B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1104 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 201 removed outlier: 4.100A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.851A pdb=" N LEU C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.585A pdb=" N VAL C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.545A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 425 through 437 removed outlier: 3.964A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 454 through 468 removed outlier: 5.033A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.829A pdb=" N LEU C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.751A pdb=" N THR C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.709A pdb=" N THR C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.710A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.763A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 646 removed outlier: 3.555A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 665 through 671 removed outlier: 3.503A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 788 removed outlier: 4.053A pdb=" N MET C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 795 Processing helix chain 'C' and resid 796 through 818 Processing helix chain 'C' and resid 821 through 843 removed outlier: 3.652A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 849 Processing helix chain 'C' and resid 853 through 890 removed outlier: 4.364A pdb=" N PHE C 869 " --> pdb=" O ILE C 865 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 913 removed outlier: 3.717A pdb=" N ILE C 899 " --> pdb=" O ARG C 895 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 957 through 987 Processing helix chain 'C' and resid 990 through 1008 removed outlier: 4.305A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1023 removed outlier: 3.590A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1069 removed outlier: 3.662A pdb=" N THR C1069 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1074 removed outlier: 4.093A pdb=" N ASP C1073 " --> pdb=" O LYS C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1104 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 201 removed outlier: 4.099A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.851A pdb=" N LEU D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.585A pdb=" N VAL D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.542A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 425 through 437 removed outlier: 3.964A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 454 through 468 removed outlier: 5.034A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.828A pdb=" N LEU D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 499 removed outlier: 3.750A pdb=" N THR D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.708A pdb=" N THR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.717A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.764A pdb=" N ALA D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 646 removed outlier: 3.555A pdb=" N GLU D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 665 through 671 removed outlier: 3.501A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 788 removed outlier: 4.052A pdb=" N MET D 788 " --> pdb=" O ARG D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 795 Processing helix chain 'D' and resid 796 through 818 Processing helix chain 'D' and resid 821 through 843 removed outlier: 3.659A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 849 Processing helix chain 'D' and resid 853 through 890 removed outlier: 4.366A pdb=" N PHE D 869 " --> pdb=" O ILE D 865 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 913 removed outlier: 3.693A pdb=" N ILE D 899 " --> pdb=" O ARG D 895 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 957 through 987 Processing helix chain 'D' and resid 990 through 1008 removed outlier: 4.306A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1023 removed outlier: 3.594A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1069 removed outlier: 3.660A pdb=" N THR D1069 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1074 removed outlier: 4.092A pdb=" N ASP D1073 " --> pdb=" O LYS D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 5.727A pdb=" N LYS A 116 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A 262 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 118 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASP A 264 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU A 120 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS A 326 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 647 through 648 removed outlier: 4.035A pdb=" N CYS A 648 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 654 " --> pdb=" O CYS A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.757A pdb=" N LYS B 116 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 262 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASP B 264 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 120 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS B 326 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 647 through 648 removed outlier: 4.078A pdb=" N CYS B 648 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 654 " --> pdb=" O CYS B 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 121 removed outlier: 5.729A pdb=" N LYS C 116 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 262 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 118 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASP C 264 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU C 120 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 326 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 647 through 648 removed outlier: 4.082A pdb=" N CYS C 648 " --> pdb=" O SER C 654 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 654 " --> pdb=" O CYS C 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 121 removed outlier: 5.750A pdb=" N LYS D 116 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 262 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASP D 264 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU D 120 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS D 326 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 647 through 648 removed outlier: 4.081A pdb=" N CYS D 648 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 654 " --> pdb=" O CYS D 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1840 hydrogen bonds defined for protein. 5460 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: 5.56 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4372 1.31 - 1.44: 7936 1.44 - 1.56: 15656 1.56 - 1.69: 16 1.69 - 1.81: 184 Bond restraints: 28164 Sorted by residual: bond pdb=" C1B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1B PIO B1201 " pdb=" O3C PIO B1201 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1B PIO C1201 " pdb=" O3C PIO C1201 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1B PIO D1201 " pdb=" O3C PIO D1201 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1A PIO C1201 " pdb=" O2C PIO C1201 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 28159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 37679 2.35 - 4.70: 402 4.70 - 7.05: 63 7.05 - 9.40: 16 9.40 - 11.76: 12 Bond angle restraints: 38172 Sorted by residual: angle pdb=" O11 PIO B1201 " pdb=" P1 PIO B1201 " pdb=" O12 PIO B1201 " ideal model delta sigma weight residual 121.09 109.33 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O11 PIO C1201 " pdb=" P1 PIO C1201 " pdb=" O12 PIO C1201 " ideal model delta sigma weight residual 121.09 109.34 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PIO A1201 " pdb=" P1 PIO A1201 " pdb=" O12 PIO A1201 " ideal model delta sigma weight residual 121.09 109.37 11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O12 PIO D1201 " ideal model delta sigma weight residual 121.09 109.43 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O1 PIO C1201 " pdb=" P1 PIO C1201 " pdb=" O13 PIO C1201 " ideal model delta sigma weight residual 97.64 109.07 -11.43 3.00e+00 1.11e-01 1.45e+01 ... (remaining 38167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14327 17.90 - 35.81: 1589 35.81 - 53.71: 385 53.71 - 71.61: 140 71.61 - 89.51: 15 Dihedral angle restraints: 16456 sinusoidal: 6504 harmonic: 9952 Sorted by residual: dihedral pdb=" CA ASP C 440 " pdb=" CB ASP C 440 " pdb=" CG ASP C 440 " pdb=" OD1 ASP C 440 " ideal model delta sinusoidal sigma weight residual -30.00 -87.72 57.72 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 440 " pdb=" CB ASP A 440 " pdb=" CG ASP A 440 " pdb=" OD1 ASP A 440 " ideal model delta sinusoidal sigma weight residual -30.00 -87.69 57.69 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP D 440 " pdb=" CB ASP D 440 " pdb=" CG ASP D 440 " pdb=" OD1 ASP D 440 " ideal model delta sinusoidal sigma weight residual -30.00 -87.68 57.68 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 16453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3273 0.036 - 0.072: 794 0.072 - 0.107: 236 0.107 - 0.143: 50 0.143 - 0.179: 7 Chirality restraints: 4360 Sorted by residual: chirality pdb=" CB VAL B1016 " pdb=" CA VAL B1016 " pdb=" CG1 VAL B1016 " pdb=" CG2 VAL B1016 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL C1016 " pdb=" CA VAL C1016 " pdb=" CG1 VAL C1016 " pdb=" CG2 VAL C1016 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL D1016 " pdb=" CA VAL D1016 " pdb=" CG1 VAL D1016 " pdb=" CG2 VAL D1016 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 4357 not shown) Planarity restraints: 4688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 835 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" CG ASP B 835 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP B 835 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 835 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1008 " 0.165 9.50e-02 1.11e+02 7.41e-02 3.70e+00 pdb=" NE ARG A1008 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1008 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A1008 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1008 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 835 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" CG ASP D 835 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP D 835 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP D 835 " -0.012 2.00e-02 2.50e+03 ... (remaining 4685 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 10068 2.88 - 3.38: 29707 3.38 - 3.89: 44138 3.89 - 4.39: 49840 4.39 - 4.90: 82056 Nonbonded interactions: 215809 Sorted by model distance: nonbonded pdb=" O ASN B 989 " pdb=" OD1 ASN B 989 " model vdw 2.372 3.040 nonbonded pdb=" O ASN D 989 " pdb=" OD1 ASN D 989 " model vdw 2.372 3.040 nonbonded pdb=" O ASN C 989 " pdb=" OD1 ASN C 989 " model vdw 2.373 3.040 nonbonded pdb=" O ASN A 989 " pdb=" OD1 ASN A 989 " model vdw 2.396 3.040 nonbonded pdb=" O13 PIO C1201 " pdb=" O2C PIO C1201 " model vdw 2.480 2.432 ... (remaining 215804 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 5.870 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 22.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28164 Z= 0.169 Angle : 0.664 11.755 38172 Z= 0.330 Chirality : 0.036 0.179 4360 Planarity : 0.004 0.074 4688 Dihedral : 16.637 89.514 9960 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 14.90 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.15), residues: 3244 helix: 2.07 (0.10), residues: 2500 sheet: -2.09 (0.36), residues: 136 loop : -1.63 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1008 TYR 0.010 0.001 TYR A 772 PHE 0.020 0.002 PHE D 779 TRP 0.008 0.001 TRP A 377 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (28164) covalent geometry : angle 0.66351 / 0.33 (38172) hydrogen bonds : bond 0.13155 / 8.74 ( 1840) hydrogen bonds : angle 4.73791 / 3.40 ( 5460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 385 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5297 (m-80) cc_final: 0.4972 (m-80) REVERT: A 118 LEU cc_start: 0.8156 (mp) cc_final: 0.7796 (tp) REVERT: A 119 ARG cc_start: 0.6912 (ttp-170) cc_final: 0.6593 (ttm170) REVERT: A 321 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7498 (mmtm) REVERT: A 353 MET cc_start: 0.6005 (mpp) cc_final: 0.5188 (mmm) REVERT: B 117 TYR cc_start: 0.5621 (m-80) cc_final: 0.5182 (m-80) REVERT: B 118 LEU cc_start: 0.8166 (mp) cc_final: 0.7797 (tp) REVERT: B 119 ARG cc_start: 0.7013 (ttp-170) cc_final: 0.6634 (ttm170) REVERT: B 353 MET cc_start: 0.5956 (mpp) cc_final: 0.5174 (mmm) REVERT: B 495 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7785 (tp30) REVERT: C 117 TYR cc_start: 0.5388 (m-80) cc_final: 0.4956 (m-80) REVERT: C 118 LEU cc_start: 0.8224 (mp) cc_final: 0.7885 (tp) REVERT: C 119 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6559 (ttm170) REVERT: C 353 MET cc_start: 0.5983 (mpp) cc_final: 0.5185 (mmm) REVERT: C 462 MET cc_start: 0.8606 (tpt) cc_final: 0.8293 (tpt) REVERT: C 495 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7777 (tp30) REVERT: D 117 TYR cc_start: 0.5356 (m-80) cc_final: 0.4897 (m-80) REVERT: D 118 LEU cc_start: 0.8047 (mp) cc_final: 0.7716 (tp) REVERT: D 119 ARG cc_start: 0.6885 (ttp-170) cc_final: 0.6535 (ttm170) REVERT: D 353 MET cc_start: 0.5948 (mpp) cc_final: 0.5172 (mmm) REVERT: D 462 MET cc_start: 0.8600 (tpt) cc_final: 0.8252 (tpt) REVERT: D 495 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7747 (tp30) outliers start: 14 outliers final: 12 residues processed: 397 average time/residue: 0.1422 time to fit residues: 93.0762 Evaluate side-chains 370 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 358 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN A 317 ASN A 559 HIS A 571 GLN A 761 HIS B 279 ASN B 559 HIS B 571 GLN B 891 GLN C 279 ASN C 559 HIS C 571 GLN D 279 ASN D 559 HIS D 571 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.201531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161587 restraints weight = 37861.859| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.18 r_work: 0.3503 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28164 Z= 0.157 Angle : 0.568 9.819 38172 Z= 0.293 Chirality : 0.039 0.156 4360 Planarity : 0.004 0.044 4688 Dihedral : 5.249 57.660 3691 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.01 % Allowed : 14.43 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.14), residues: 3244 helix: 2.05 (0.10), residues: 2512 sheet: -1.36 (0.37), residues: 136 loop : -1.70 (0.20), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1008 TYR 0.015 0.001 TYR B 772 PHE 0.016 0.002 PHE C 847 TRP 0.022 0.001 TRP C 877 HIS 0.002 0.001 HIS D 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (28164) covalent geometry : angle 0.56756 / 0.29 (38172) hydrogen bonds : bond 0.05483 / 3.64 ( 1840) hydrogen bonds : angle 3.86745 / 2.79 ( 5460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5343 (m-80) cc_final: 0.4883 (m-10) REVERT: A 118 LEU cc_start: 0.8133 (mp) cc_final: 0.7930 (tp) REVERT: A 119 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6438 (ppt170) REVERT: A 321 LYS cc_start: 0.7922 (mmtp) cc_final: 0.7640 (mmtm) REVERT: A 353 MET cc_start: 0.6044 (mpp) cc_final: 0.5182 (mmm) REVERT: A 866 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 118 LEU cc_start: 0.8150 (mp) cc_final: 0.7911 (tp) REVERT: B 119 ARG cc_start: 0.7159 (ttp-170) cc_final: 0.6431 (ppt170) REVERT: B 321 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7511 (mmtm) REVERT: B 353 MET cc_start: 0.6028 (mpp) cc_final: 0.5184 (mmm) REVERT: B 866 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8357 (t0) REVERT: C 119 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6346 (ppt170) REVERT: C 321 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7602 (mmtm) REVERT: C 353 MET cc_start: 0.6006 (mpp) cc_final: 0.5171 (mmm) REVERT: C 462 MET cc_start: 0.8445 (tpt) cc_final: 0.8203 (tpt) REVERT: D 118 LEU cc_start: 0.8140 (mp) cc_final: 0.7888 (tp) REVERT: D 119 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6392 (ppt170) REVERT: D 321 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7589 (mmtm) REVERT: D 353 MET cc_start: 0.6016 (mpp) cc_final: 0.5166 (mmm) REVERT: D 462 MET cc_start: 0.8442 (tpt) cc_final: 0.8199 (tpt) REVERT: D 809 PHE cc_start: 0.6365 (t80) cc_final: 0.6112 (t80) outliers start: 59 outliers final: 47 residues processed: 417 average time/residue: 0.1465 time to fit residues: 99.9294 Evaluate side-chains 395 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 975 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 253 optimal weight: 40.0000 chunk 121 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.200291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.160538 restraints weight = 37559.057| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.16 r_work: 0.3484 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28164 Z= 0.171 Angle : 0.563 8.695 38172 Z= 0.292 Chirality : 0.040 0.178 4360 Planarity : 0.004 0.051 4688 Dihedral : 5.300 56.177 3688 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.76 % Allowed : 15.72 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3244 helix: 1.99 (0.10), residues: 2512 sheet: -1.01 (0.42), residues: 136 loop : -1.88 (0.20), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1008 TYR 0.037 0.002 TYR D 772 PHE 0.033 0.002 PHE C 881 TRP 0.017 0.001 TRP D 877 HIS 0.004 0.001 HIS A 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (28164) covalent geometry : angle 0.56271 / 0.29 (38172) hydrogen bonds : bond 0.05518 / 3.67 ( 1840) hydrogen bonds : angle 3.84998 / 2.79 ( 5460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 370 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5243 (m-80) cc_final: 0.4778 (m-10) REVERT: A 118 LEU cc_start: 0.8122 (mp) cc_final: 0.7884 (tp) REVERT: A 119 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6429 (ppt170) REVERT: A 321 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7742 (mmtm) REVERT: A 353 MET cc_start: 0.6077 (mpp) cc_final: 0.5154 (mmm) REVERT: A 746 ILE cc_start: 0.8885 (pt) cc_final: 0.8616 (pt) REVERT: B 118 LEU cc_start: 0.8205 (mp) cc_final: 0.7961 (tp) REVERT: B 119 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.6458 (ppt170) REVERT: B 190 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7610 (ptmm) REVERT: B 353 MET cc_start: 0.6099 (mpp) cc_final: 0.5199 (mmm) REVERT: B 746 ILE cc_start: 0.8899 (pt) cc_final: 0.8631 (pt) REVERT: B 1059 MET cc_start: 0.8292 (mmm) cc_final: 0.8075 (mmt) REVERT: C 117 TYR cc_start: 0.5256 (m-80) cc_final: 0.4827 (m-10) REVERT: C 119 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6480 (ttp-170) REVERT: C 353 MET cc_start: 0.6100 (mpp) cc_final: 0.5196 (mmm) REVERT: C 462 MET cc_start: 0.8486 (tpt) cc_final: 0.8190 (tpt) REVERT: C 746 ILE cc_start: 0.8894 (pt) cc_final: 0.8637 (pt) REVERT: C 1059 MET cc_start: 0.8305 (mmm) cc_final: 0.8090 (mmt) REVERT: D 118 LEU cc_start: 0.8178 (mp) cc_final: 0.7916 (tp) REVERT: D 119 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6446 (ppt170) REVERT: D 353 MET cc_start: 0.6095 (mpp) cc_final: 0.5191 (mmm) REVERT: D 462 MET cc_start: 0.8497 (tpt) cc_final: 0.8205 (tpt) REVERT: D 1059 MET cc_start: 0.8323 (mmm) cc_final: 0.8116 (mmt) outliers start: 81 outliers final: 45 residues processed: 430 average time/residue: 0.1528 time to fit residues: 106.0075 Evaluate side-chains 388 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 899 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 103 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 997 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 ASN B 997 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 968 ASN C 997 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 968 ASN D 997 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.199613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160135 restraints weight = 37482.611| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.16 r_work: 0.3482 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 28164 Z= 0.222 Angle : 0.626 10.627 38172 Z= 0.323 Chirality : 0.042 0.264 4360 Planarity : 0.005 0.061 4688 Dihedral : 5.414 59.323 3682 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.55 % Allowed : 16.00 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3244 helix: 1.75 (0.10), residues: 2508 sheet: -0.95 (0.44), residues: 136 loop : -2.04 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1008 TYR 0.037 0.002 TYR A 772 PHE 0.024 0.002 PHE A 165 TRP 0.018 0.002 TRP B 877 HIS 0.005 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (28164) covalent geometry : angle 0.62614 / 0.32 (38172) hydrogen bonds : bond 0.06182 / 4.10 ( 1840) hydrogen bonds : angle 3.96554 / 2.87 ( 5460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 365 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5079 (m-80) cc_final: 0.4633 (m-10) REVERT: A 118 LEU cc_start: 0.8139 (mp) cc_final: 0.7905 (tp) REVERT: A 119 ARG cc_start: 0.7252 (ttp-170) cc_final: 0.6510 (ppt170) REVERT: A 353 MET cc_start: 0.6044 (mpp) cc_final: 0.5097 (mmm) REVERT: A 746 ILE cc_start: 0.8903 (pt) cc_final: 0.8625 (pt) REVERT: A 994 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.6430 (t-100) REVERT: B 117 TYR cc_start: 0.5097 (m-80) cc_final: 0.4323 (m-10) REVERT: B 118 LEU cc_start: 0.8110 (mp) cc_final: 0.7829 (tp) REVERT: B 119 ARG cc_start: 0.7265 (ttp-170) cc_final: 0.6504 (ppt170) REVERT: B 190 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7662 (ptmm) REVERT: B 321 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7653 (mmtm) REVERT: B 353 MET cc_start: 0.6095 (mpp) cc_final: 0.5199 (mmm) REVERT: B 746 ILE cc_start: 0.8925 (pt) cc_final: 0.8503 (pt) REVERT: B 750 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 781 ASP cc_start: 0.7853 (t70) cc_final: 0.7393 (t0) REVERT: B 994 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6465 (t-100) REVERT: C 117 TYR cc_start: 0.4965 (m-80) cc_final: 0.4335 (m-10) REVERT: C 119 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.7015 (ptm160) REVERT: C 321 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7682 (mmtm) REVERT: C 353 MET cc_start: 0.6080 (mpp) cc_final: 0.5161 (mmm) REVERT: C 462 MET cc_start: 0.8575 (tpt) cc_final: 0.8156 (tpt) REVERT: C 746 ILE cc_start: 0.8911 (pt) cc_final: 0.8540 (pt) REVERT: C 750 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 994 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.6483 (t-100) REVERT: D 117 TYR cc_start: 0.5113 (m-80) cc_final: 0.4328 (m-10) REVERT: D 118 LEU cc_start: 0.8125 (mp) cc_final: 0.7856 (tp) REVERT: D 119 ARG cc_start: 0.7254 (ttp-170) cc_final: 0.6494 (ppt170) REVERT: D 321 LYS cc_start: 0.7923 (mmtp) cc_final: 0.7699 (mmtm) REVERT: D 353 MET cc_start: 0.6071 (mpp) cc_final: 0.5144 (mmm) REVERT: D 462 MET cc_start: 0.8570 (tpt) cc_final: 0.8145 (tpt) REVERT: D 781 ASP cc_start: 0.7843 (t70) cc_final: 0.7539 (t0) REVERT: D 994 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.6461 (t-100) outliers start: 104 outliers final: 66 residues processed: 443 average time/residue: 0.1610 time to fit residues: 118.1640 Evaluate side-chains 416 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 28 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 40.0000 chunk 179 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.199061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160644 restraints weight = 37535.438| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.07 r_work: 0.3485 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28164 Z= 0.221 Angle : 0.625 10.657 38172 Z= 0.319 Chirality : 0.041 0.173 4360 Planarity : 0.005 0.065 4688 Dihedral : 5.471 59.770 3682 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.82 % Allowed : 16.61 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3244 helix: 1.60 (0.10), residues: 2504 sheet: -0.99 (0.44), residues: 136 loop : -2.01 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1008 TYR 0.037 0.002 TYR A 772 PHE 0.021 0.002 PHE A 165 TRP 0.018 0.002 TRP C 377 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (28164) covalent geometry : angle 0.62451 / 0.32 (38172) hydrogen bonds : bond 0.06050 / 4.01 ( 1840) hydrogen bonds : angle 3.94330 / 2.86 ( 5460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 351 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5157 (m-80) cc_final: 0.4516 (m-10) REVERT: A 118 LEU cc_start: 0.8118 (mp) cc_final: 0.7830 (tp) REVERT: A 119 ARG cc_start: 0.7282 (ttp-170) cc_final: 0.6544 (ppt170) REVERT: A 353 MET cc_start: 0.6075 (mpp) cc_final: 0.5112 (mmm) REVERT: A 451 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5926 (mtt180) REVERT: A 746 ILE cc_start: 0.8911 (pt) cc_final: 0.8534 (pt) REVERT: A 750 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 994 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.6536 (t-100) REVERT: B 117 TYR cc_start: 0.5083 (m-80) cc_final: 0.4177 (m-10) REVERT: B 118 LEU cc_start: 0.8079 (mp) cc_final: 0.7781 (tp) REVERT: B 119 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6548 (ppt170) REVERT: B 353 MET cc_start: 0.6115 (mpp) cc_final: 0.5199 (mmm) REVERT: B 746 ILE cc_start: 0.8933 (pt) cc_final: 0.8708 (pt) REVERT: B 781 ASP cc_start: 0.7814 (t70) cc_final: 0.7483 (t0) REVERT: B 994 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.6574 (t-100) REVERT: B 1009 LEU cc_start: 0.6657 (mm) cc_final: 0.6291 (mp) REVERT: C 119 ARG cc_start: 0.7344 (ttp-170) cc_final: 0.6481 (ppt170) REVERT: C 321 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7677 (mmtm) REVERT: C 353 MET cc_start: 0.6128 (mpp) cc_final: 0.5220 (mmm) REVERT: C 451 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5957 (mtt180) REVERT: C 462 MET cc_start: 0.8547 (tpt) cc_final: 0.8172 (tpt) REVERT: C 746 ILE cc_start: 0.8938 (pt) cc_final: 0.8566 (pt) REVERT: C 750 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 994 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.6599 (t-100) REVERT: C 1009 LEU cc_start: 0.6661 (mm) cc_final: 0.6291 (mp) REVERT: D 117 TYR cc_start: 0.5097 (m-80) cc_final: 0.4190 (m-10) REVERT: D 118 LEU cc_start: 0.8069 (mp) cc_final: 0.7771 (tp) REVERT: D 119 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.6545 (ppt170) REVERT: D 321 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7682 (mmtm) REVERT: D 353 MET cc_start: 0.6095 (mpp) cc_final: 0.5166 (mmm) REVERT: D 462 MET cc_start: 0.8549 (tpt) cc_final: 0.8172 (tpt) REVERT: D 750 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8350 (mp) REVERT: D 870 PHE cc_start: 0.7049 (m-10) cc_final: 0.6795 (m-10) REVERT: D 994 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.6571 (t-100) REVERT: D 1009 LEU cc_start: 0.6668 (mm) cc_final: 0.6288 (mp) outliers start: 112 outliers final: 77 residues processed: 439 average time/residue: 0.1608 time to fit residues: 116.4439 Evaluate side-chains 424 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 748 PHE Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 164 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.200169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161081 restraints weight = 37330.493| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.03 r_work: 0.3512 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28164 Z= 0.177 Angle : 0.587 11.169 38172 Z= 0.300 Chirality : 0.040 0.166 4360 Planarity : 0.004 0.063 4688 Dihedral : 5.383 58.970 3682 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.68 % Allowed : 17.74 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3244 helix: 1.68 (0.10), residues: 2504 sheet: -0.86 (0.45), residues: 136 loop : -2.00 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1008 TYR 0.040 0.002 TYR B 772 PHE 0.037 0.002 PHE D 881 TRP 0.017 0.001 TRP D 377 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (28164) covalent geometry : angle 0.58700 / 0.30 (38172) hydrogen bonds : bond 0.05512 / 3.66 ( 1840) hydrogen bonds : angle 3.83422 / 2.78 ( 5460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 357 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5130 (m-80) cc_final: 0.4553 (m-10) REVERT: A 118 LEU cc_start: 0.8092 (mp) cc_final: 0.7776 (tp) REVERT: A 119 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6606 (ppt170) REVERT: A 353 MET cc_start: 0.6107 (mpp) cc_final: 0.5152 (mmm) REVERT: A 746 ILE cc_start: 0.8857 (pt) cc_final: 0.8483 (pt) REVERT: A 750 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 994 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.6560 (t-100) REVERT: B 117 TYR cc_start: 0.4995 (m-80) cc_final: 0.4224 (m-10) REVERT: B 118 LEU cc_start: 0.8053 (mp) cc_final: 0.7729 (tp) REVERT: B 119 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6525 (ppt170) REVERT: B 353 MET cc_start: 0.6116 (mpp) cc_final: 0.5209 (mmm) REVERT: B 496 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 746 ILE cc_start: 0.8880 (pt) cc_final: 0.8510 (pt) REVERT: B 750 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 878 MET cc_start: 0.7766 (ptt) cc_final: 0.7312 (ptt) REVERT: B 994 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.6556 (t-100) REVERT: B 1009 LEU cc_start: 0.6679 (mm) cc_final: 0.6308 (mp) REVERT: C 119 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7041 (ptm160) REVERT: C 353 MET cc_start: 0.6113 (mpp) cc_final: 0.5218 (mmm) REVERT: C 462 MET cc_start: 0.8533 (tpt) cc_final: 0.8187 (tpt) REVERT: C 496 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 746 ILE cc_start: 0.8886 (pt) cc_final: 0.8512 (pt) REVERT: C 750 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8282 (mp) REVERT: C 994 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.6586 (t-100) REVERT: C 1009 LEU cc_start: 0.6681 (mm) cc_final: 0.6312 (mp) REVERT: D 117 TYR cc_start: 0.5034 (m-80) cc_final: 0.4262 (m-10) REVERT: D 118 LEU cc_start: 0.8073 (mp) cc_final: 0.7751 (tp) REVERT: D 119 ARG cc_start: 0.7262 (ttp-170) cc_final: 0.6538 (ppt170) REVERT: D 353 MET cc_start: 0.6118 (mpp) cc_final: 0.5202 (mmm) REVERT: D 462 MET cc_start: 0.8540 (tpt) cc_final: 0.8195 (tpt) REVERT: D 496 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8766 (mp) REVERT: D 750 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8249 (mp) REVERT: D 911 MET cc_start: 0.3423 (mmm) cc_final: 0.3214 (tpt) REVERT: D 994 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.6560 (t-100) REVERT: D 1009 LEU cc_start: 0.6641 (mm) cc_final: 0.6276 (mp) outliers start: 108 outliers final: 83 residues processed: 440 average time/residue: 0.1580 time to fit residues: 116.7203 Evaluate side-chains 435 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 341 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 748 PHE Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 899 ILE Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 183 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 249 optimal weight: 30.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 HIS B 317 ASN C 317 ASN D 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.203053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163516 restraints weight = 37258.110| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.72 r_work: 0.3578 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28164 Z= 0.129 Angle : 0.570 12.412 38172 Z= 0.285 Chirality : 0.038 0.162 4360 Planarity : 0.004 0.057 4688 Dihedral : 5.242 59.440 3682 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.59 % Allowed : 18.96 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3244 helix: 1.81 (0.10), residues: 2512 sheet: -0.61 (0.45), residues: 136 loop : -1.99 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1008 TYR 0.037 0.001 TYR A 772 PHE 0.012 0.001 PHE A 847 TRP 0.020 0.001 TRP A 877 HIS 0.003 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (28164) covalent geometry : angle 0.57030 / 0.29 (38172) hydrogen bonds : bond 0.04740 / 3.15 ( 1840) hydrogen bonds : angle 3.69576 / 2.68 ( 5460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 363 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8030 (mp) cc_final: 0.7685 (tp) REVERT: A 119 ARG cc_start: 0.7225 (ttp-170) cc_final: 0.6561 (ppt170) REVERT: A 353 MET cc_start: 0.6060 (mpp) cc_final: 0.5136 (mmm) REVERT: A 746 ILE cc_start: 0.8816 (pt) cc_final: 0.8444 (pt) REVERT: A 750 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 878 MET cc_start: 0.7555 (ptt) cc_final: 0.7248 (ptt) REVERT: A 911 MET cc_start: 0.3550 (mmm) cc_final: 0.3335 (tpt) REVERT: A 994 TRP cc_start: 0.8111 (OUTLIER) cc_final: 0.6548 (t-100) REVERT: B 117 TYR cc_start: 0.4924 (m-80) cc_final: 0.4236 (m-10) REVERT: B 118 LEU cc_start: 0.8012 (mp) cc_final: 0.7653 (tp) REVERT: B 119 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6526 (ppt170) REVERT: B 353 MET cc_start: 0.6120 (mpp) cc_final: 0.5255 (mmm) REVERT: B 496 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 746 ILE cc_start: 0.8813 (pt) cc_final: 0.8446 (pt) REVERT: B 750 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8224 (mp) REVERT: B 994 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.6565 (t-100) REVERT: B 1009 LEU cc_start: 0.6640 (mm) cc_final: 0.6317 (mp) REVERT: C 119 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.7013 (ptm160) REVERT: C 353 MET cc_start: 0.6129 (mpp) cc_final: 0.5259 (mmm) REVERT: C 462 MET cc_start: 0.8493 (tpt) cc_final: 0.8193 (tpt) REVERT: C 496 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 746 ILE cc_start: 0.8802 (pt) cc_final: 0.8427 (mt) REVERT: C 994 TRP cc_start: 0.8133 (OUTLIER) cc_final: 0.6584 (t-100) REVERT: C 1009 LEU cc_start: 0.6641 (mm) cc_final: 0.6318 (mp) REVERT: D 117 TYR cc_start: 0.4957 (m-80) cc_final: 0.4263 (m-10) REVERT: D 118 LEU cc_start: 0.8059 (mp) cc_final: 0.7695 (tp) REVERT: D 119 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6525 (ppt170) REVERT: D 353 MET cc_start: 0.6133 (mpp) cc_final: 0.5247 (mmm) REVERT: D 462 MET cc_start: 0.8493 (tpt) cc_final: 0.8193 (tpt) REVERT: D 496 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (mp) REVERT: D 746 ILE cc_start: 0.8680 (pt) cc_final: 0.8229 (pt) REVERT: D 750 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 911 MET cc_start: 0.3568 (mmm) cc_final: 0.3366 (tpt) REVERT: D 994 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.6575 (t-100) REVERT: D 1009 LEU cc_start: 0.6639 (mm) cc_final: 0.6310 (mp) outliers start: 76 outliers final: 54 residues processed: 415 average time/residue: 0.1429 time to fit residues: 99.3614 Evaluate side-chains 417 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 0.9980 chunk 286 optimal weight: 0.0970 chunk 71 optimal weight: 20.0000 chunk 177 optimal weight: 30.0000 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 671 GLN B 138 HIS B 671 GLN C 138 HIS C 671 GLN D 138 HIS D 671 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.206598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.168059 restraints weight = 37358.394| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.78 r_work: 0.3690 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28164 Z= 0.108 Angle : 0.546 10.994 38172 Z= 0.273 Chirality : 0.037 0.143 4360 Planarity : 0.004 0.050 4688 Dihedral : 5.053 59.128 3682 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.42 % Allowed : 18.93 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3244 helix: 1.95 (0.10), residues: 2512 sheet: -0.37 (0.46), residues: 136 loop : -1.91 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1008 TYR 0.041 0.001 TYR D 772 PHE 0.016 0.001 PHE D 869 TRP 0.014 0.001 TRP A 453 HIS 0.002 0.000 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (28164) covalent geometry : angle 0.54617 / 0.27 (38172) hydrogen bonds : bond 0.04023 / 2.68 ( 1840) hydrogen bonds : angle 3.61091 / 2.62 ( 5460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 364 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7999 (mp) cc_final: 0.7657 (tp) REVERT: A 119 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6587 (ppt170) REVERT: A 353 MET cc_start: 0.6095 (mpp) cc_final: 0.5161 (mmm) REVERT: A 631 GLU cc_start: 0.8118 (tp30) cc_final: 0.7854 (tp30) REVERT: A 746 ILE cc_start: 0.8824 (pt) cc_final: 0.8405 (mt) REVERT: A 911 MET cc_start: 0.3631 (mmm) cc_final: 0.3427 (tpt) REVERT: A 994 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.6592 (t-100) REVERT: B 117 TYR cc_start: 0.4908 (m-80) cc_final: 0.4387 (m-10) REVERT: B 118 LEU cc_start: 0.8032 (mp) cc_final: 0.7658 (tp) REVERT: B 119 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6568 (ppt170) REVERT: B 353 MET cc_start: 0.6035 (mpp) cc_final: 0.5208 (mmm) REVERT: B 462 MET cc_start: 0.8469 (tpt) cc_final: 0.8104 (tpt) REVERT: B 496 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 746 ILE cc_start: 0.8819 (pt) cc_final: 0.8292 (mt) REVERT: B 750 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8224 (mp) REVERT: B 871 LEU cc_start: 0.7490 (mt) cc_final: 0.7100 (mt) REVERT: B 994 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.6586 (t-100) REVERT: B 1009 LEU cc_start: 0.6545 (mm) cc_final: 0.6251 (mp) REVERT: C 117 TYR cc_start: 0.4983 (m-80) cc_final: 0.4364 (m-10) REVERT: C 119 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.7065 (ptm160) REVERT: C 353 MET cc_start: 0.6108 (mpp) cc_final: 0.5256 (mmm) REVERT: C 462 MET cc_start: 0.8430 (tpt) cc_final: 0.8193 (tpt) REVERT: C 496 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 746 ILE cc_start: 0.8796 (pt) cc_final: 0.8470 (mt) REVERT: C 871 LEU cc_start: 0.7526 (mt) cc_final: 0.7176 (mt) REVERT: C 994 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.6622 (t-100) REVERT: C 1009 LEU cc_start: 0.6561 (mm) cc_final: 0.6269 (mp) REVERT: D 117 TYR cc_start: 0.4900 (m-80) cc_final: 0.4361 (m-10) REVERT: D 118 LEU cc_start: 0.8019 (mp) cc_final: 0.7668 (tp) REVERT: D 119 ARG cc_start: 0.7191 (ttp-170) cc_final: 0.6540 (ppt170) REVERT: D 353 MET cc_start: 0.6092 (mpp) cc_final: 0.5246 (mmm) REVERT: D 462 MET cc_start: 0.8446 (tpt) cc_final: 0.8213 (tpt) REVERT: D 496 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 746 ILE cc_start: 0.8696 (pt) cc_final: 0.8294 (mt) REVERT: D 994 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.6607 (t-100) REVERT: D 1009 LEU cc_start: 0.6525 (mm) cc_final: 0.6221 (mp) outliers start: 71 outliers final: 53 residues processed: 404 average time/residue: 0.1379 time to fit residues: 93.3882 Evaluate side-chains 408 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 994 TRP Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 136 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.203033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163337 restraints weight = 37306.871| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.75 r_work: 0.3582 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28164 Z= 0.147 Angle : 0.585 12.156 38172 Z= 0.293 Chirality : 0.039 0.149 4360 Planarity : 0.004 0.055 4688 Dihedral : 5.117 58.904 3682 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.76 % Allowed : 18.72 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.15), residues: 3244 helix: 1.92 (0.10), residues: 2508 sheet: -0.33 (0.46), residues: 136 loop : -1.91 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1008 TYR 0.041 0.001 TYR A 772 PHE 0.018 0.001 PHE B 869 TRP 0.016 0.001 TRP B 377 HIS 0.012 0.001 HIS B 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (28164) covalent geometry : angle 0.58521 / 0.29 (38172) hydrogen bonds : bond 0.04756 / 3.16 ( 1840) hydrogen bonds : angle 3.69506 / 2.68 ( 5460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7974 (mp) cc_final: 0.7656 (tp) REVERT: A 119 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6589 (ppt170) REVERT: A 353 MET cc_start: 0.6037 (mpp) cc_final: 0.5109 (mmm) REVERT: A 496 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 631 GLU cc_start: 0.8131 (tp30) cc_final: 0.7882 (tp30) REVERT: A 994 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.6559 (t-100) REVERT: B 117 TYR cc_start: 0.4873 (m-80) cc_final: 0.4259 (m-10) REVERT: B 118 LEU cc_start: 0.8051 (mp) cc_final: 0.7686 (tp) REVERT: B 119 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6570 (ppt170) REVERT: B 353 MET cc_start: 0.6113 (mpp) cc_final: 0.5244 (mmm) REVERT: B 496 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 746 ILE cc_start: 0.8843 (pt) cc_final: 0.8246 (mt) REVERT: B 750 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 994 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.6564 (t-100) REVERT: B 1009 LEU cc_start: 0.6556 (mm) cc_final: 0.6231 (mp) REVERT: C 119 ARG cc_start: 0.7357 (ttp-170) cc_final: 0.7067 (ptm160) REVERT: C 321 LYS cc_start: 0.7755 (mmtp) cc_final: 0.7443 (mmtm) REVERT: C 353 MET cc_start: 0.6119 (mpp) cc_final: 0.5236 (mmm) REVERT: C 462 MET cc_start: 0.8503 (tpt) cc_final: 0.8198 (tpt) REVERT: C 496 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 746 ILE cc_start: 0.8783 (pt) cc_final: 0.8436 (mt) REVERT: C 878 MET cc_start: 0.7596 (ptp) cc_final: 0.7143 (ptp) REVERT: C 994 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.6606 (t-100) REVERT: C 1009 LEU cc_start: 0.6579 (mm) cc_final: 0.6252 (mp) REVERT: D 117 TYR cc_start: 0.4914 (m-80) cc_final: 0.4304 (m-10) REVERT: D 118 LEU cc_start: 0.8023 (mp) cc_final: 0.7672 (tp) REVERT: D 119 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6553 (ppt170) REVERT: D 321 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7468 (mmtm) REVERT: D 353 MET cc_start: 0.6070 (mpp) cc_final: 0.5219 (mmm) REVERT: D 462 MET cc_start: 0.8504 (tpt) cc_final: 0.8194 (tpt) REVERT: D 496 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8739 (mp) REVERT: D 746 ILE cc_start: 0.8675 (pt) cc_final: 0.8417 (pt) REVERT: D 878 MET cc_start: 0.7647 (ptp) cc_final: 0.7209 (ptp) REVERT: D 994 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.6586 (t-100) REVERT: D 1009 LEU cc_start: 0.6545 (mm) cc_final: 0.6220 (mp) outliers start: 81 outliers final: 59 residues processed: 404 average time/residue: 0.1669 time to fit residues: 112.8711 Evaluate side-chains 418 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 70 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 389 HIS C 389 HIS D 389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.203261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.163973 restraints weight = 37401.419| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.83 r_work: 0.3577 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28164 Z= 0.137 Angle : 0.580 12.508 38172 Z= 0.290 Chirality : 0.038 0.143 4360 Planarity : 0.004 0.055 4688 Dihedral : 5.126 59.647 3682 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.42 % Allowed : 19.20 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3244 helix: 1.90 (0.10), residues: 2508 sheet: -0.69 (0.43), residues: 156 loop : -1.86 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1008 TYR 0.022 0.001 TYR C 981 PHE 0.018 0.001 PHE A 869 TRP 0.024 0.001 TRP A 877 HIS 0.009 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (28164) covalent geometry : angle 0.57966 / 0.29 (38172) hydrogen bonds : bond 0.04627 / 3.08 ( 1840) hydrogen bonds : angle 3.68675 / 2.68 ( 5460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 360 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8012 (mp) cc_final: 0.7784 (tp) REVERT: A 119 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.6535 (ppt170) REVERT: A 353 MET cc_start: 0.6034 (mpp) cc_final: 0.5097 (mmm) REVERT: A 496 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8741 (mp) REVERT: A 771 LEU cc_start: 0.7936 (tt) cc_final: 0.7586 (tp) REVERT: A 994 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.6571 (t-100) REVERT: B 117 TYR cc_start: 0.4880 (m-80) cc_final: 0.4258 (m-10) REVERT: B 118 LEU cc_start: 0.8041 (mp) cc_final: 0.7657 (tp) REVERT: B 119 ARG cc_start: 0.7217 (ttp-170) cc_final: 0.6540 (ppt170) REVERT: B 353 MET cc_start: 0.6081 (mpp) cc_final: 0.5233 (mmm) REVERT: B 496 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8754 (mp) REVERT: B 746 ILE cc_start: 0.8837 (pt) cc_final: 0.8291 (mt) REVERT: B 750 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 994 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.6591 (t-100) REVERT: B 1009 LEU cc_start: 0.6536 (mm) cc_final: 0.6223 (mp) REVERT: C 119 ARG cc_start: 0.7308 (ttp-170) cc_final: 0.6695 (ttp-170) REVERT: C 321 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7437 (mmtm) REVERT: C 353 MET cc_start: 0.6116 (mpp) cc_final: 0.5248 (mmm) REVERT: C 462 MET cc_start: 0.8499 (tpt) cc_final: 0.8199 (tpt) REVERT: C 496 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 746 ILE cc_start: 0.8755 (pt) cc_final: 0.8434 (mt) REVERT: C 771 LEU cc_start: 0.7945 (tt) cc_final: 0.7610 (tp) REVERT: C 863 MET cc_start: 0.7532 (mtm) cc_final: 0.7289 (mtt) REVERT: C 994 TRP cc_start: 0.8208 (OUTLIER) cc_final: 0.6609 (t-100) REVERT: C 1009 LEU cc_start: 0.6550 (mm) cc_final: 0.6236 (mp) REVERT: D 117 TYR cc_start: 0.4923 (m-80) cc_final: 0.4305 (m-10) REVERT: D 118 LEU cc_start: 0.8010 (mp) cc_final: 0.7650 (tp) REVERT: D 119 ARG cc_start: 0.7174 (ttp-170) cc_final: 0.6552 (ppt170) REVERT: D 321 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7468 (mmtm) REVERT: D 353 MET cc_start: 0.6119 (mpp) cc_final: 0.5256 (mmm) REVERT: D 462 MET cc_start: 0.8510 (tpt) cc_final: 0.8211 (tpt) REVERT: D 496 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8747 (mp) REVERT: D 746 ILE cc_start: 0.8656 (pt) cc_final: 0.8412 (pt) REVERT: D 771 LEU cc_start: 0.7930 (tt) cc_final: 0.7584 (tp) REVERT: D 994 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.6596 (t-100) REVERT: D 1009 LEU cc_start: 0.6556 (mm) cc_final: 0.6240 (mp) outliers start: 71 outliers final: 59 residues processed: 404 average time/residue: 0.1481 time to fit residues: 100.6899 Evaluate side-chains 422 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 354 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 994 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN B 671 GLN C 671 GLN D 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.200167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160783 restraints weight = 37169.106| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.11 r_work: 0.3506 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 28164 Z= 0.201 Angle : 0.641 12.662 38172 Z= 0.322 Chirality : 0.041 0.180 4360 Planarity : 0.004 0.061 4688 Dihedral : 5.266 57.287 3682 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.59 % Allowed : 19.13 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.15), residues: 3244 helix: 1.73 (0.10), residues: 2512 sheet: -0.83 (0.42), residues: 156 loop : -1.85 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1008 TYR 0.022 0.002 TYR C 981 PHE 0.019 0.002 PHE A 165 TRP 0.021 0.002 TRP B 377 HIS 0.004 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (28164) covalent geometry : angle 0.64144 / 0.32 (38172) hydrogen bonds : bond 0.05587 / 3.71 ( 1840) hydrogen bonds : angle 3.86228 / 2.80 ( 5460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.80 seconds wall clock time: 103 minutes 41.47 seconds (6221.47 seconds total)