Starting phenix.real_space_refine on Thu Jun 26 07:08:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.map" model { file = "/net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wre_32724/06_2025/7wre_32724.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.07, per 1000 atoms: 0.53 Number of scatterers: 30468 At special positions: 0 Unit cell: (153.114, 153.114, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.38 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.38 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.38 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.38 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: 7.03 Conformation dependent library (CDL) restraints added in 3.5 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 4 sheets defined 70.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.787A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.677A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.654A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.677A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.522A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.597A 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 removed outlier: 3.795A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 4.051A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU A 769 " --> pdb=" O HIS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 847 removed outlier: 4.298A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 860 removed outlier: 4.559A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix removed outlier: 3.573A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.787A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.677A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.654A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG B 368 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.563A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.655A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.677A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.521A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.597A 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 removed outlier: 3.795A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 4.052A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU B 769 " --> pdb=" O HIS B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 847 removed outlier: 4.297A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 852 through 860 removed outlier: 4.559A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix removed outlier: 3.572A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.787A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.677A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.653A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG C 368 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.563A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.676A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.522A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.597A 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 removed outlier: 3.795A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 4.051A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 788 removed outlier: 3.521A pdb=" N LEU C 769 " --> pdb=" O HIS C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 847 removed outlier: 4.297A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 852 through 860 removed outlier: 4.560A pdb=" N LYS C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.655A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix removed outlier: 3.572A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1006 removed outlier: 3.668A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1070 removed outlier: 3.978A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.791A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.787A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.677A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.653A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG D 368 " --> pdb=" O THR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.564A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.677A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.522A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.598A 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 removed outlier: 3.795A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 4.052A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU D 769 " --> pdb=" O HIS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 847 removed outlier: 4.298A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 852 through 860 removed outlier: 4.560A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix removed outlier: 3.573A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 177 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE A 212 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 327 " --> pdb=" O THR A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 177 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 212 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 327 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 177 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE C 212 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 327 " --> pdb=" O THR C 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 121 removed outlier: 6.170A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 177 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 212 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 327 " --> pdb=" O THR D 392 " (cutoff:3.500A) 1784 hydrogen bonds defined for protein. 5292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4892 1.31 - 1.44: 8876 1.44 - 1.57: 17208 1.57 - 1.70: 0 1.70 - 1.83: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.17e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.486 -0.131 2.00e-02 2.50e+03 4.29e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 39533 2.16 - 4.33: 2281 4.33 - 6.49: 298 6.49 - 8.66: 100 8.66 - 10.82: 40 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N SER C 917 " pdb=" CA SER C 917 " pdb=" C SER C 917 " ideal model delta sigma weight residual 111.36 121.66 -10.30 1.09e+00 8.42e-01 8.93e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 111.36 121.63 -10.27 1.09e+00 8.42e-01 8.88e+01 angle pdb=" N SER D 917 " pdb=" CA SER D 917 " pdb=" C SER D 917 " ideal model delta sigma weight residual 111.36 121.50 -10.14 1.09e+00 8.42e-01 8.65e+01 angle pdb=" N SER B 917 " pdb=" CA SER B 917 " pdb=" C SER B 917 " ideal model delta sigma weight residual 111.36 121.35 -9.99 1.09e+00 8.42e-01 8.41e+01 angle pdb=" N ASP A 920 " pdb=" CA ASP A 920 " pdb=" C ASP A 920 " ideal model delta sigma weight residual 111.36 120.96 -9.60 1.09e+00 8.42e-01 7.76e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 16879 14.80 - 29.60: 1111 29.60 - 44.40: 262 44.40 - 59.20: 20 59.20 - 74.01: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA LYS D 573 " pdb=" C LYS D 573 " pdb=" N LYS D 574 " pdb=" CA LYS D 574 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS A 573 " pdb=" C LYS A 573 " pdb=" N LYS A 574 " pdb=" CA LYS A 574 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS C 573 " pdb=" C LYS C 573 " pdb=" N LYS C 574 " pdb=" CA LYS C 574 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3237 0.065 - 0.130: 1186 0.130 - 0.195: 237 0.195 - 0.260: 31 0.260 - 0.325: 17 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA SER A 917 " pdb=" N SER A 917 " pdb=" C SER A 917 " pdb=" CB SER A 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA SER C 917 " pdb=" N SER C 917 " pdb=" C SER C 917 " pdb=" CB SER C 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA SER D 917 " pdb=" N SER D 917 " pdb=" C SER D 917 " pdb=" CB SER D 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 752 " 0.002 2.00e-02 2.50e+03 2.36e-02 9.75e+00 pdb=" CG PHE B 752 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 752 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE B 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 752 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 752 " -0.002 2.00e-02 2.50e+03 2.34e-02 9.56e+00 pdb=" CG PHE A 752 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 752 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 752 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 752 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 752 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 752 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 752 " 0.002 2.00e-02 2.50e+03 2.33e-02 9.52e+00 pdb=" CG PHE C 752 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 752 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 752 " -0.006 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4616 2.75 - 3.29: 29038 3.29 - 3.82: 49502 3.82 - 4.36: 58912 4.36 - 4.90: 99149 Nonbonded interactions: 241217 Sorted by model distance: nonbonded pdb=" OD1 ASP A 920 " pdb=" NH2 ARG B 901 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASP C 920 " pdb=" NH2 ARG D 901 " model vdw 2.213 3.120 nonbonded pdb=" NH2 ARG A 901 " pdb=" OD1 ASP D 920 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP B 920 " pdb=" NH2 ARG C 901 " model vdw 2.251 3.120 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 206 " model vdw 2.259 3.040 ... (remaining 241212 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 65.240 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:18.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.013 0.354 31192 Z= 0.567 Angle : 1.210 25.269 42260 Z= 0.670 Chirality : 0.068 0.325 4708 Planarity : 0.007 0.066 5280 Dihedral : 10.862 74.005 11212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.15 % Favored : 93.52 % Rotamer: Outliers : 0.24 % Allowed : 3.25 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.11), residues: 3656 helix: -1.98 (0.08), residues: 2400 sheet: -2.21 (0.32), residues: 192 loop : -3.18 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 651 HIS 0.016 0.004 HIS A 765 PHE 0.043 0.004 PHE C 832 TYR 0.051 0.004 TYR A 772 ARG 0.010 0.001 ARG B 829 Details of bonding type rmsd hydrogen bonds : bond 0.17052 ( 1784) hydrogen bonds : angle 6.96062 ( 5292) SS BOND : bond 0.35249 ( 4) SS BOND : angle 19.71736 ( 8) covalent geometry : bond 0.01264 (31188) covalent geometry : angle 1.17886 (42252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 659 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.8251 (mpp) cc_final: 0.7924 (mtt) REVERT: A 198 ASP cc_start: 0.8432 (m-30) cc_final: 0.7986 (m-30) REVERT: B 189 MET cc_start: 0.8248 (mpp) cc_final: 0.7927 (mtt) REVERT: C 189 MET cc_start: 0.8260 (mpp) cc_final: 0.7931 (mtt) REVERT: D 189 MET cc_start: 0.8253 (mpp) cc_final: 0.7920 (mtt) REVERT: D 198 ASP cc_start: 0.8428 (m-30) cc_final: 0.7978 (m-30) outliers start: 8 outliers final: 4 residues processed: 667 average time/residue: 1.5980 time to fit residues: 1233.1288 Evaluate side-chains 391 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 257 HIS A 259 HIS A 270 HIS A 294 ASN A 667 HIS A 671 GLN A 675 GLN A 741 ASN B 136 HIS B 257 HIS B 259 HIS B 270 HIS B 294 ASN B 667 HIS B 671 GLN B 675 GLN C 257 HIS C 259 HIS C 270 HIS C 294 ASN C 667 HIS C 671 GLN C 675 GLN D 136 HIS D 257 HIS D 259 HIS D 270 HIS D 294 ASN D 438 GLN D 667 HIS D 671 GLN D 675 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086881 restraints weight = 68910.506| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.77 r_work: 0.3207 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31192 Z= 0.176 Angle : 0.696 7.802 42260 Z= 0.370 Chirality : 0.042 0.148 4708 Planarity : 0.005 0.081 5280 Dihedral : 6.161 54.436 4032 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.67 % Allowed : 11.45 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3656 helix: -0.06 (0.10), residues: 2436 sheet: -2.22 (0.35), residues: 192 loop : -2.72 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 453 HIS 0.006 0.001 HIS B 138 PHE 0.019 0.002 PHE B 874 TYR 0.017 0.002 TYR B 787 ARG 0.009 0.001 ARG D1079 Details of bonding type rmsd hydrogen bonds : bond 0.05542 ( 1784) hydrogen bonds : angle 4.64445 ( 5292) SS BOND : bond 0.00533 ( 4) SS BOND : angle 2.51177 ( 8) covalent geometry : bond 0.00405 (31188) covalent geometry : angle 0.69501 (42252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 457 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7824 (mpp) cc_final: 0.7500 (mtm) REVERT: A 194 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8725 (mt-10) REVERT: A 282 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: A 353 MET cc_start: 0.7751 (mpp) cc_final: 0.7454 (pmm) REVERT: A 401 ASP cc_start: 0.9058 (t0) cc_final: 0.8837 (t0) REVERT: A 462 MET cc_start: 0.8904 (tmm) cc_final: 0.8658 (tmm) REVERT: A 518 ASP cc_start: 0.8469 (t0) cc_final: 0.8075 (t0) REVERT: A 631 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8276 (tt0) REVERT: A 942 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: A 1066 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8778 (mtmm) REVERT: B 189 MET cc_start: 0.7837 (mpp) cc_final: 0.7534 (mtm) REVERT: B 191 TYR cc_start: 0.8235 (t80) cc_final: 0.8032 (t80) REVERT: B 194 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8795 (mt-10) REVERT: B 282 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: B 353 MET cc_start: 0.7748 (mpp) cc_final: 0.7486 (pmm) REVERT: B 401 ASP cc_start: 0.9065 (t0) cc_final: 0.8839 (t0) REVERT: B 462 MET cc_start: 0.8903 (tmm) cc_final: 0.8690 (tmm) REVERT: B 518 ASP cc_start: 0.8466 (t0) cc_final: 0.8065 (t0) REVERT: B 631 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8273 (tt0) REVERT: B 689 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (p0) REVERT: B 1066 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8771 (mtmm) REVERT: C 189 MET cc_start: 0.7830 (mpp) cc_final: 0.7510 (mtm) REVERT: C 191 TYR cc_start: 0.8242 (t80) cc_final: 0.8025 (t80) REVERT: C 194 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8801 (mt-10) REVERT: C 282 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 353 MET cc_start: 0.7750 (mpp) cc_final: 0.7492 (pmm) REVERT: C 401 ASP cc_start: 0.9078 (t0) cc_final: 0.8848 (t0) REVERT: C 462 MET cc_start: 0.8897 (tmm) cc_final: 0.8650 (tmm) REVERT: C 518 ASP cc_start: 0.8439 (t0) cc_final: 0.8044 (t0) REVERT: C 631 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8323 (tt0) REVERT: C 689 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8204 (p0) REVERT: C 1059 MET cc_start: 0.7978 (mpp) cc_final: 0.7702 (mpp) REVERT: C 1066 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8774 (mtmm) REVERT: D 189 MET cc_start: 0.7834 (mpp) cc_final: 0.7511 (mtm) REVERT: D 191 TYR cc_start: 0.8239 (t80) cc_final: 0.8037 (t80) REVERT: D 194 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8725 (mt-10) REVERT: D 282 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: D 353 MET cc_start: 0.7752 (mpp) cc_final: 0.7445 (pmm) REVERT: D 401 ASP cc_start: 0.9061 (t0) cc_final: 0.8842 (t0) REVERT: D 457 ASP cc_start: 0.7735 (t0) cc_final: 0.7323 (t0) REVERT: D 462 MET cc_start: 0.8911 (tmm) cc_final: 0.8667 (tmm) REVERT: D 518 ASP cc_start: 0.8478 (t0) cc_final: 0.8277 (t0) REVERT: D 631 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8266 (tt0) REVERT: D 689 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8152 (p0) REVERT: D 942 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: D 1066 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8769 (mtmm) outliers start: 89 outliers final: 20 residues processed: 519 average time/residue: 1.4562 time to fit residues: 885.9793 Evaluate side-chains 377 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 348 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 81 optimal weight: 0.9990 chunk 209 optimal weight: 0.0270 chunk 263 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 328 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 GLN B 256 ASN B 438 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN B 997 GLN C 136 HIS C 256 ASN C 438 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 ASN C 997 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 ASN D 997 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.124859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086970 restraints weight = 69310.578| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.84 r_work: 0.3210 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31192 Z= 0.150 Angle : 0.624 7.592 42260 Z= 0.329 Chirality : 0.041 0.146 4708 Planarity : 0.004 0.064 5280 Dihedral : 5.726 46.935 4024 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.94 % Allowed : 13.64 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3656 helix: 0.74 (0.10), residues: 2460 sheet: -1.85 (0.36), residues: 188 loop : -2.43 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 453 HIS 0.005 0.001 HIS D 138 PHE 0.025 0.001 PHE D1021 TYR 0.017 0.002 TYR A 191 ARG 0.008 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 1784) hydrogen bonds : angle 4.31627 ( 5292) SS BOND : bond 0.01156 ( 4) SS BOND : angle 3.50233 ( 8) covalent geometry : bond 0.00345 (31188) covalent geometry : angle 0.62182 (42252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 418 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 189 MET cc_start: 0.7747 (mpp) cc_final: 0.7482 (mtm) REVERT: A 191 TYR cc_start: 0.8247 (t80) cc_final: 0.7944 (t80) REVERT: A 194 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8826 (mt-10) REVERT: A 282 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8055 (pp20) REVERT: A 451 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (pmt-80) REVERT: A 462 MET cc_start: 0.8939 (tmm) cc_final: 0.8729 (tmm) REVERT: A 989 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (t0) REVERT: A 1023 MET cc_start: 0.7508 (mmp) cc_final: 0.6345 (ttm) REVERT: B 141 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (p) REVERT: B 189 MET cc_start: 0.7733 (mpp) cc_final: 0.7451 (mtm) REVERT: B 191 TYR cc_start: 0.8216 (t80) cc_final: 0.7965 (t80) REVERT: B 194 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8792 (mt-10) REVERT: B 282 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8054 (pp20) REVERT: B 451 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7760 (pmt-80) REVERT: B 462 MET cc_start: 0.8907 (tmm) cc_final: 0.8678 (tmm) REVERT: B 518 ASP cc_start: 0.8378 (t0) cc_final: 0.8166 (t70) REVERT: B 689 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8224 (p0) REVERT: B 1023 MET cc_start: 0.7445 (mmp) cc_final: 0.6270 (ttm) REVERT: C 141 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 189 MET cc_start: 0.7755 (mpp) cc_final: 0.7486 (mtm) REVERT: C 191 TYR cc_start: 0.8203 (t80) cc_final: 0.7981 (t80) REVERT: C 194 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8792 (mt-10) REVERT: C 282 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: C 451 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7751 (pmt-80) REVERT: C 462 MET cc_start: 0.8927 (tmm) cc_final: 0.8716 (tmm) REVERT: C 518 ASP cc_start: 0.8370 (t0) cc_final: 0.8157 (t70) REVERT: C 631 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8395 (tt0) REVERT: C 689 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8202 (p0) REVERT: C 989 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7848 (t0) REVERT: C 1023 MET cc_start: 0.7510 (mmp) cc_final: 0.6343 (ttm) REVERT: D 141 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8481 (p) REVERT: D 189 MET cc_start: 0.7767 (mpp) cc_final: 0.7445 (mtm) REVERT: D 191 TYR cc_start: 0.8215 (t80) cc_final: 0.7990 (t80) REVERT: D 194 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8780 (mt-10) REVERT: D 282 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8051 (pp20) REVERT: D 395 LYS cc_start: 0.8619 (mppt) cc_final: 0.8300 (mppt) REVERT: D 457 ASP cc_start: 0.7663 (t0) cc_final: 0.7247 (t0) REVERT: D 462 MET cc_start: 0.8951 (tmm) cc_final: 0.8741 (tmm) REVERT: D 518 ASP cc_start: 0.8431 (t0) cc_final: 0.8030 (t0) REVERT: D 596 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8829 (tptm) REVERT: D 689 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (p0) REVERT: D 1023 MET cc_start: 0.7517 (mmp) cc_final: 0.6342 (ttm) outliers start: 98 outliers final: 40 residues processed: 486 average time/residue: 1.3441 time to fit residues: 778.7564 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 335 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 973 ASN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D 609 ASN D 973 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088130 restraints weight = 69032.358| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.74 r_work: 0.3231 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.128 Angle : 0.596 8.253 42260 Z= 0.312 Chirality : 0.040 0.141 4708 Planarity : 0.004 0.036 5280 Dihedral : 5.452 46.668 4024 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.64 % Allowed : 14.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3656 helix: 1.15 (0.10), residues: 2476 sheet: -1.93 (0.38), residues: 176 loop : -2.13 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 453 HIS 0.005 0.001 HIS A 138 PHE 0.024 0.001 PHE D 779 TYR 0.020 0.002 TYR D 646 ARG 0.008 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 1784) hydrogen bonds : angle 4.15611 ( 5292) SS BOND : bond 0.00612 ( 4) SS BOND : angle 2.10605 ( 8) covalent geometry : bond 0.00288 (31188) covalent geometry : angle 0.59564 (42252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 363 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 162 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.8215 (mtm-85) REVERT: A 189 MET cc_start: 0.7723 (mpp) cc_final: 0.7475 (mtm) REVERT: A 191 TYR cc_start: 0.8222 (t80) cc_final: 0.7975 (t80) REVERT: A 194 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8815 (mt-10) REVERT: A 353 MET cc_start: 0.7735 (mpp) cc_final: 0.7422 (pmm) REVERT: A 360 ARG cc_start: 0.8709 (ptm160) cc_final: 0.8504 (ppp80) REVERT: A 451 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7801 (pmt-80) REVERT: A 731 PHE cc_start: 0.8227 (m-10) cc_final: 0.7535 (t80) REVERT: A 942 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (pt0) REVERT: A 1023 MET cc_start: 0.7471 (mmp) cc_final: 0.6337 (ttm) REVERT: A 1059 MET cc_start: 0.7832 (mpp) cc_final: 0.7178 (pmm) REVERT: B 141 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 189 MET cc_start: 0.7728 (mpp) cc_final: 0.7471 (mtm) REVERT: B 194 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8728 (mt-10) REVERT: B 353 MET cc_start: 0.7746 (mpp) cc_final: 0.7422 (pmm) REVERT: B 360 ARG cc_start: 0.8709 (ptm160) cc_final: 0.8504 (ppp80) REVERT: B 451 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7811 (pmt-80) REVERT: B 615 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8217 (tm-30) REVERT: B 689 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8111 (p0) REVERT: B 731 PHE cc_start: 0.8226 (m-10) cc_final: 0.7571 (t80) REVERT: B 942 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8688 (pt0) REVERT: B 1023 MET cc_start: 0.7462 (mmp) cc_final: 0.6338 (ttm) REVERT: B 1059 MET cc_start: 0.7824 (mpp) cc_final: 0.7228 (pmm) REVERT: C 141 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (p) REVERT: C 179 ILE cc_start: 0.8645 (pt) cc_final: 0.8348 (pp) REVERT: C 189 MET cc_start: 0.7738 (mpp) cc_final: 0.7503 (mtm) REVERT: C 194 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8747 (mt-10) REVERT: C 353 MET cc_start: 0.7752 (mpp) cc_final: 0.7425 (pmm) REVERT: C 360 ARG cc_start: 0.8702 (ptm160) cc_final: 0.8495 (ppp80) REVERT: C 451 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7836 (pmt-80) REVERT: C 615 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8214 (tm-30) REVERT: C 689 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8124 (p0) REVERT: C 731 PHE cc_start: 0.8194 (m-10) cc_final: 0.7536 (t80) REVERT: C 942 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: C 1023 MET cc_start: 0.7461 (mmp) cc_final: 0.6327 (ttm) REVERT: D 141 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8463 (p) REVERT: D 179 ILE cc_start: 0.8647 (pt) cc_final: 0.8376 (pp) REVERT: D 189 MET cc_start: 0.7761 (mpp) cc_final: 0.7477 (mtm) REVERT: D 194 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8741 (mt-10) REVERT: D 353 MET cc_start: 0.7734 (mpp) cc_final: 0.7410 (pmm) REVERT: D 457 ASP cc_start: 0.7670 (t0) cc_final: 0.7285 (t0) REVERT: D 518 ASP cc_start: 0.8440 (t0) cc_final: 0.8198 (t70) REVERT: D 689 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8098 (p0) REVERT: D 731 PHE cc_start: 0.8229 (m-10) cc_final: 0.7542 (t80) REVERT: D 942 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8675 (pt0) REVERT: D 1023 MET cc_start: 0.7473 (mmp) cc_final: 0.6327 (ttm) REVERT: D 1059 MET cc_start: 0.7830 (mpp) cc_final: 0.7160 (pmm) outliers start: 121 outliers final: 42 residues processed: 458 average time/residue: 1.3520 time to fit residues: 735.2349 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1066 LYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1066 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 136 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 352 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 355 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 992 GLN B 449 ASN B 992 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 HIS C 992 GLN D 572 ASN D 761 HIS D 973 ASN D 992 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084864 restraints weight = 68830.532| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.74 r_work: 0.3170 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31192 Z= 0.217 Angle : 0.656 9.822 42260 Z= 0.343 Chirality : 0.043 0.152 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.408 48.757 4024 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.40 % Allowed : 15.35 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3656 helix: 1.35 (0.10), residues: 2456 sheet: -1.92 (0.36), residues: 188 loop : -2.16 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 786 HIS 0.005 0.001 HIS B 138 PHE 0.032 0.002 PHE A1021 TYR 0.015 0.002 TYR A 186 ARG 0.005 0.001 ARG D1083 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 1784) hydrogen bonds : angle 4.29285 ( 5292) SS BOND : bond 0.01269 ( 4) SS BOND : angle 4.52975 ( 8) covalent geometry : bond 0.00518 (31188) covalent geometry : angle 0.65263 (42252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 368 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 189 MET cc_start: 0.7822 (mpp) cc_final: 0.7529 (mtm) REVERT: A 353 MET cc_start: 0.7792 (mpp) cc_final: 0.7498 (pmm) REVERT: A 360 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8358 (ppp80) REVERT: A 731 PHE cc_start: 0.8092 (m-10) cc_final: 0.7522 (t80) REVERT: A 942 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: A 985 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 1023 MET cc_start: 0.7463 (mmp) cc_final: 0.6371 (ttp) REVERT: B 141 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8545 (p) REVERT: B 189 MET cc_start: 0.7825 (mpp) cc_final: 0.7508 (mtm) REVERT: B 194 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8733 (mt-10) REVERT: B 353 MET cc_start: 0.7757 (mpp) cc_final: 0.7463 (pmm) REVERT: B 360 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8359 (ppp80) REVERT: B 689 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 731 PHE cc_start: 0.8089 (m-10) cc_final: 0.7530 (t80) REVERT: B 942 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8698 (pt0) REVERT: B 985 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 1023 MET cc_start: 0.7459 (mmp) cc_final: 0.6369 (ttp) REVERT: C 141 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 189 MET cc_start: 0.7795 (mpp) cc_final: 0.7463 (mtm) REVERT: C 194 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8739 (mt-10) REVERT: C 353 MET cc_start: 0.7768 (mpp) cc_final: 0.7472 (pmm) REVERT: C 360 ARG cc_start: 0.8661 (ptm160) cc_final: 0.8370 (ppp80) REVERT: C 689 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (p0) REVERT: C 731 PHE cc_start: 0.8082 (m-10) cc_final: 0.7530 (t80) REVERT: C 942 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: C 985 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8501 (mp) REVERT: C 1023 MET cc_start: 0.7462 (mmp) cc_final: 0.6356 (ttp) REVERT: C 1059 MET cc_start: 0.7880 (mpp) cc_final: 0.7254 (pmm) REVERT: D 141 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8565 (p) REVERT: D 189 MET cc_start: 0.7823 (mpp) cc_final: 0.7550 (mtm) REVERT: D 194 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8767 (mt-10) REVERT: D 353 MET cc_start: 0.7779 (mpp) cc_final: 0.7478 (pmm) REVERT: D 457 ASP cc_start: 0.7816 (t0) cc_final: 0.7402 (t0) REVERT: D 462 MET cc_start: 0.8912 (tmm) cc_final: 0.8657 (tmm) REVERT: D 689 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (p0) REVERT: D 731 PHE cc_start: 0.8205 (m-10) cc_final: 0.7524 (t80) REVERT: D 942 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: D 985 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 1023 MET cc_start: 0.7467 (mmp) cc_final: 0.6355 (ttp) outliers start: 113 outliers final: 58 residues processed: 454 average time/residue: 1.3224 time to fit residues: 718.6440 Evaluate side-chains 405 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 332 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 0.0770 chunk 188 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 992 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN C 992 GLN D 973 ASN D 992 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087403 restraints weight = 68811.945| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.76 r_work: 0.3215 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31192 Z= 0.132 Angle : 0.603 11.328 42260 Z= 0.315 Chirality : 0.041 0.161 4708 Planarity : 0.004 0.030 5280 Dihedral : 5.358 51.215 4024 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.79 % Allowed : 17.43 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3656 helix: 1.58 (0.10), residues: 2468 sheet: -1.80 (0.38), residues: 176 loop : -1.93 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 453 HIS 0.004 0.001 HIS A 138 PHE 0.026 0.001 PHE D 779 TYR 0.012 0.001 TYR A 727 ARG 0.006 0.000 ARG B 452 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 1784) hydrogen bonds : angle 4.07114 ( 5292) SS BOND : bond 0.00646 ( 4) SS BOND : angle 2.86129 ( 8) covalent geometry : bond 0.00298 (31188) covalent geometry : angle 0.60160 (42252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 359 time to evaluate : 3.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 189 MET cc_start: 0.7741 (mpp) cc_final: 0.7449 (mtm) REVERT: A 194 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8765 (mt-10) REVERT: A 353 MET cc_start: 0.7753 (mpp) cc_final: 0.7503 (pmm) REVERT: A 360 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8414 (ppp80) REVERT: A 731 PHE cc_start: 0.8096 (m-10) cc_final: 0.7534 (t80) REVERT: A 942 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8670 (pt0) REVERT: A 985 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 1023 MET cc_start: 0.7444 (mmp) cc_final: 0.6372 (ttp) REVERT: A 1059 MET cc_start: 0.7881 (mpp) cc_final: 0.7301 (pmm) REVERT: B 141 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 189 MET cc_start: 0.7665 (mpp) cc_final: 0.7406 (mtm) REVERT: B 194 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 353 MET cc_start: 0.7770 (mpp) cc_final: 0.7508 (pmm) REVERT: B 360 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8412 (ppp80) REVERT: B 689 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8052 (p0) REVERT: B 731 PHE cc_start: 0.8093 (m-10) cc_final: 0.7546 (t80) REVERT: B 942 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8686 (pt0) REVERT: B 985 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 1023 MET cc_start: 0.7442 (mmp) cc_final: 0.6370 (ttp) REVERT: B 1059 MET cc_start: 0.7876 (mpp) cc_final: 0.7280 (pmm) REVERT: C 141 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 179 ILE cc_start: 0.8675 (pt) cc_final: 0.8417 (pp) REVERT: C 189 MET cc_start: 0.7766 (mpp) cc_final: 0.7484 (mtm) REVERT: C 194 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8778 (mt-10) REVERT: C 353 MET cc_start: 0.7765 (mpp) cc_final: 0.7512 (pmm) REVERT: C 360 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8413 (ppp80) REVERT: C 689 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (p0) REVERT: C 731 PHE cc_start: 0.8087 (m-10) cc_final: 0.7552 (t80) REVERT: C 942 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: C 985 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 1023 MET cc_start: 0.7444 (mmp) cc_final: 0.6355 (ttp) REVERT: C 1059 MET cc_start: 0.7821 (mpp) cc_final: 0.7107 (pmm) REVERT: D 141 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8489 (p) REVERT: D 189 MET cc_start: 0.7780 (mpp) cc_final: 0.7518 (mtm) REVERT: D 194 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8796 (mt-10) REVERT: D 353 MET cc_start: 0.7767 (mpp) cc_final: 0.7511 (pmm) REVERT: D 457 ASP cc_start: 0.7749 (t0) cc_final: 0.7360 (t0) REVERT: D 689 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8070 (p0) REVERT: D 731 PHE cc_start: 0.8170 (m-10) cc_final: 0.7536 (t80) REVERT: D 942 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 985 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 1023 MET cc_start: 0.7447 (mmp) cc_final: 0.6354 (ttp) REVERT: D 1059 MET cc_start: 0.7880 (mpp) cc_final: 0.7294 (pmm) outliers start: 93 outliers final: 41 residues processed: 434 average time/residue: 1.5458 time to fit residues: 806.4397 Evaluate side-chains 378 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 7.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 23 optimal weight: 30.0000 chunk 230 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 136 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 334 optimal weight: 0.0060 chunk 286 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 overall best weight: 3.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 HIS A 992 GLN B 572 ASN B 761 HIS B 992 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 973 ASN C 992 GLN D 973 ASN D 992 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.122731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084343 restraints weight = 69289.488| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.87 r_work: 0.3160 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31192 Z= 0.202 Angle : 0.650 11.871 42260 Z= 0.337 Chirality : 0.043 0.160 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.349 54.529 4024 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.88 % Allowed : 17.97 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3656 helix: 1.63 (0.10), residues: 2460 sheet: -1.83 (0.39), residues: 176 loop : -1.97 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 786 HIS 0.005 0.001 HIS A 138 PHE 0.038 0.002 PHE A1021 TYR 0.012 0.002 TYR B 621 ARG 0.008 0.001 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 1784) hydrogen bonds : angle 4.18241 ( 5292) SS BOND : bond 0.00703 ( 4) SS BOND : angle 3.22422 ( 8) covalent geometry : bond 0.00480 (31188) covalent geometry : angle 0.64830 (42252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 341 time to evaluate : 3.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 189 MET cc_start: 0.7767 (mpp) cc_final: 0.7519 (mtm) REVERT: A 194 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 353 MET cc_start: 0.7822 (mpp) cc_final: 0.7495 (pmm) REVERT: A 360 ARG cc_start: 0.8712 (ptm160) cc_final: 0.8483 (ppp80) REVERT: A 731 PHE cc_start: 0.8103 (m-10) cc_final: 0.7505 (t80) REVERT: A 942 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8751 (pt0) REVERT: A 985 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8513 (mp) REVERT: A 1023 MET cc_start: 0.7458 (mmp) cc_final: 0.6361 (ttp) REVERT: A 1059 MET cc_start: 0.7816 (mpp) cc_final: 0.7180 (pmm) REVERT: A 1076 GLU cc_start: 0.8963 (pp20) cc_final: 0.8599 (pm20) REVERT: B 141 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 189 MET cc_start: 0.7865 (mpp) cc_final: 0.7493 (mtm) REVERT: B 194 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8752 (mt-10) REVERT: B 353 MET cc_start: 0.7806 (mpp) cc_final: 0.7463 (pmm) REVERT: B 360 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8475 (ppp80) REVERT: B 689 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8096 (p0) REVERT: B 731 PHE cc_start: 0.8117 (m-10) cc_final: 0.7511 (t80) REVERT: B 942 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: B 985 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 1023 MET cc_start: 0.7400 (mmp) cc_final: 0.6313 (ttp) REVERT: B 1059 MET cc_start: 0.7830 (mpp) cc_final: 0.7186 (pmm) REVERT: C 141 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8540 (p) REVERT: C 179 ILE cc_start: 0.8722 (pt) cc_final: 0.8374 (pp) REVERT: C 194 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8777 (mt-10) REVERT: C 353 MET cc_start: 0.7825 (mpp) cc_final: 0.7528 (pmm) REVERT: C 360 ARG cc_start: 0.8719 (ptm160) cc_final: 0.8488 (ppp80) REVERT: C 689 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8087 (p0) REVERT: C 731 PHE cc_start: 0.8106 (m-10) cc_final: 0.7497 (t80) REVERT: C 942 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8718 (pt0) REVERT: C 985 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 1023 MET cc_start: 0.7400 (mmp) cc_final: 0.6305 (ttp) REVERT: D 141 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8541 (p) REVERT: D 194 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8739 (mt-10) REVERT: D 353 MET cc_start: 0.7821 (mpp) cc_final: 0.7496 (pmm) REVERT: D 457 ASP cc_start: 0.7923 (t0) cc_final: 0.7479 (t0) REVERT: D 689 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8118 (p0) REVERT: D 731 PHE cc_start: 0.8114 (m-10) cc_final: 0.7514 (t80) REVERT: D 942 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8709 (pt0) REVERT: D 985 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 1023 MET cc_start: 0.7396 (mmp) cc_final: 0.6290 (ttp) REVERT: D 1059 MET cc_start: 0.7818 (mpp) cc_final: 0.7187 (pmm) outliers start: 96 outliers final: 54 residues processed: 419 average time/residue: 1.6716 time to fit residues: 859.9194 Evaluate side-chains 396 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 7.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 185 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN A 992 GLN B 992 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN C 992 GLN D 973 ASN D 992 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086617 restraints weight = 68828.690| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.81 r_work: 0.3197 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31192 Z= 0.138 Angle : 0.614 11.317 42260 Z= 0.321 Chirality : 0.041 0.153 4708 Planarity : 0.004 0.068 5280 Dihedral : 5.230 51.503 4024 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.52 % Allowed : 18.00 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3656 helix: 1.79 (0.10), residues: 2460 sheet: -1.71 (0.37), residues: 188 loop : -1.91 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 786 HIS 0.004 0.001 HIS A 138 PHE 0.028 0.001 PHE B 779 TYR 0.012 0.001 TYR B 727 ARG 0.005 0.000 ARG C 688 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 1784) hydrogen bonds : angle 4.02555 ( 5292) SS BOND : bond 0.00591 ( 4) SS BOND : angle 2.47563 ( 8) covalent geometry : bond 0.00318 (31188) covalent geometry : angle 0.61359 (42252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 359 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7706 (mpp) cc_final: 0.7497 (mtm) REVERT: A 194 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8760 (mt-10) REVERT: A 353 MET cc_start: 0.7786 (mpp) cc_final: 0.7501 (pmm) REVERT: A 360 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8495 (ppp80) REVERT: A 731 PHE cc_start: 0.8103 (m-10) cc_final: 0.7530 (t80) REVERT: A 942 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: A 985 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 1023 MET cc_start: 0.7498 (mmp) cc_final: 0.6424 (ttp) REVERT: A 1059 MET cc_start: 0.7858 (mpp) cc_final: 0.7106 (pmm) REVERT: A 1078 MET cc_start: 0.7389 (mmt) cc_final: 0.7039 (mmt) REVERT: B 189 MET cc_start: 0.7676 (mpp) cc_final: 0.7373 (mtm) REVERT: B 191 TYR cc_start: 0.8376 (t80) cc_final: 0.8079 (t80) REVERT: B 194 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8769 (mt-10) REVERT: B 353 MET cc_start: 0.7801 (mpp) cc_final: 0.7502 (pmm) REVERT: B 360 ARG cc_start: 0.8731 (ptm160) cc_final: 0.8500 (ppp80) REVERT: B 689 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 731 PHE cc_start: 0.8115 (m-10) cc_final: 0.7539 (t80) REVERT: B 942 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: B 985 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 1023 MET cc_start: 0.7396 (mmp) cc_final: 0.6318 (ttp) REVERT: B 1059 MET cc_start: 0.7856 (mpp) cc_final: 0.7098 (pmm) REVERT: C 162 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8303 (ttm-80) REVERT: C 179 ILE cc_start: 0.8686 (pt) cc_final: 0.8456 (pp) REVERT: C 189 MET cc_start: 0.7305 (mtm) cc_final: 0.6934 (mtt) REVERT: C 194 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8796 (mt-10) REVERT: C 353 MET cc_start: 0.7792 (mpp) cc_final: 0.7502 (pmm) REVERT: C 360 ARG cc_start: 0.8733 (ptm160) cc_final: 0.8499 (ppp80) REVERT: C 689 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8013 (p0) REVERT: C 731 PHE cc_start: 0.8121 (m-10) cc_final: 0.7545 (t80) REVERT: C 942 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8705 (pt0) REVERT: C 985 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 1023 MET cc_start: 0.7402 (mmp) cc_final: 0.6313 (ttp) REVERT: C 1059 MET cc_start: 0.7978 (mpp) cc_final: 0.7458 (pmm) REVERT: D 189 MET cc_start: 0.7452 (mtm) cc_final: 0.7038 (mtt) REVERT: D 194 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8774 (mt-10) REVERT: D 353 MET cc_start: 0.7788 (mpp) cc_final: 0.7504 (pmm) REVERT: D 457 ASP cc_start: 0.7846 (t0) cc_final: 0.7470 (t0) REVERT: D 689 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8069 (p0) REVERT: D 731 PHE cc_start: 0.8112 (m-10) cc_final: 0.7540 (t80) REVERT: D 942 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8654 (pt0) REVERT: D 985 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 1023 MET cc_start: 0.7437 (mmp) cc_final: 0.6370 (ttp) REVERT: D 1059 MET cc_start: 0.7843 (mpp) cc_final: 0.7147 (pmm) REVERT: D 1076 GLU cc_start: 0.8866 (pp20) cc_final: 0.8474 (pm20) outliers start: 84 outliers final: 47 residues processed: 429 average time/residue: 1.2480 time to fit residues: 643.0817 Evaluate side-chains 389 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1015 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 176 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 992 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN D 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.124449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086626 restraints weight = 68555.730| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.82 r_work: 0.3198 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31192 Z= 0.144 Angle : 0.630 10.760 42260 Z= 0.330 Chirality : 0.042 0.151 4708 Planarity : 0.004 0.055 5280 Dihedral : 5.286 52.630 4024 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.37 % Allowed : 18.57 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3656 helix: 1.82 (0.10), residues: 2460 sheet: -1.70 (0.37), residues: 188 loop : -1.94 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 786 HIS 0.005 0.001 HIS B 257 PHE 0.041 0.001 PHE A1021 TYR 0.011 0.001 TYR A 727 ARG 0.014 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1784) hydrogen bonds : angle 4.00249 ( 5292) SS BOND : bond 0.00264 ( 4) SS BOND : angle 4.59385 ( 8) covalent geometry : bond 0.00334 (31188) covalent geometry : angle 0.62726 (42252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 343 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8794 (mt-10) REVERT: A 353 MET cc_start: 0.7824 (mpp) cc_final: 0.7541 (pmm) REVERT: A 360 ARG cc_start: 0.8748 (ptm160) cc_final: 0.8518 (ppp80) REVERT: A 731 PHE cc_start: 0.8104 (m-10) cc_final: 0.7531 (t80) REVERT: A 985 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 1023 MET cc_start: 0.7443 (mmp) cc_final: 0.6394 (ttp) REVERT: B 162 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8539 (mtm-85) REVERT: B 189 MET cc_start: 0.7739 (mpp) cc_final: 0.7429 (mtm) REVERT: B 194 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8791 (mt-10) REVERT: B 353 MET cc_start: 0.7812 (mpp) cc_final: 0.7513 (pmm) REVERT: B 360 ARG cc_start: 0.8733 (ptm160) cc_final: 0.8502 (ppp80) REVERT: B 457 ASP cc_start: 0.7814 (t0) cc_final: 0.7592 (t0) REVERT: B 518 ASP cc_start: 0.8303 (t0) cc_final: 0.8077 (t0) REVERT: B 689 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8038 (p0) REVERT: B 731 PHE cc_start: 0.8130 (m-10) cc_final: 0.7559 (t80) REVERT: B 942 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: B 985 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 1023 MET cc_start: 0.7474 (mmp) cc_final: 0.6428 (ttp) REVERT: C 179 ILE cc_start: 0.8732 (pt) cc_final: 0.8511 (pp) REVERT: C 189 MET cc_start: 0.7376 (mtm) cc_final: 0.7012 (mtt) REVERT: C 194 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 353 MET cc_start: 0.7835 (mpp) cc_final: 0.7545 (pmm) REVERT: C 360 ARG cc_start: 0.8758 (ptm160) cc_final: 0.8524 (ppp80) REVERT: C 518 ASP cc_start: 0.8292 (t0) cc_final: 0.8064 (t0) REVERT: C 689 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8039 (p0) REVERT: C 731 PHE cc_start: 0.8136 (m-10) cc_final: 0.7563 (t80) REVERT: C 942 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: C 985 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8509 (mp) REVERT: C 1023 MET cc_start: 0.7469 (mmp) cc_final: 0.6414 (ttp) REVERT: C 1059 MET cc_start: 0.7956 (mpp) cc_final: 0.7448 (pmm) REVERT: D 189 MET cc_start: 0.7442 (mtm) cc_final: 0.7032 (mtt) REVERT: D 194 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8772 (mt-10) REVERT: D 353 MET cc_start: 0.7825 (mpp) cc_final: 0.7543 (pmm) REVERT: D 457 ASP cc_start: 0.7920 (t0) cc_final: 0.7522 (t0) REVERT: D 689 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8073 (p0) REVERT: D 731 PHE cc_start: 0.8127 (m-10) cc_final: 0.7555 (t80) REVERT: D 985 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8518 (mp) REVERT: D 1023 MET cc_start: 0.7467 (mmp) cc_final: 0.6417 (ttp) REVERT: D 1076 GLU cc_start: 0.8900 (pp20) cc_final: 0.8498 (pm20) outliers start: 79 outliers final: 50 residues processed: 407 average time/residue: 1.3287 time to fit residues: 657.1129 Evaluate side-chains 392 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1015 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 167 optimal weight: 0.0770 chunk 352 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 371 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 449 ASN C 992 GLN D 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087480 restraints weight = 68302.435| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.81 r_work: 0.3218 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31192 Z= 0.134 Angle : 0.634 11.870 42260 Z= 0.332 Chirality : 0.041 0.172 4708 Planarity : 0.004 0.060 5280 Dihedral : 5.179 50.025 4024 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.95 % Allowed : 19.20 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3656 helix: 1.86 (0.10), residues: 2460 sheet: -1.68 (0.37), residues: 188 loop : -1.91 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 786 HIS 0.004 0.001 HIS A 138 PHE 0.029 0.001 PHE A 779 TYR 0.012 0.001 TYR D 191 ARG 0.013 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 1784) hydrogen bonds : angle 3.96482 ( 5292) SS BOND : bond 0.00477 ( 4) SS BOND : angle 4.18155 ( 8) covalent geometry : bond 0.00307 (31188) covalent geometry : angle 0.63115 (42252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 353 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7428 (mtm) cc_final: 0.7105 (mtt) REVERT: A 194 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8796 (mt-10) REVERT: A 353 MET cc_start: 0.7785 (mpp) cc_final: 0.7504 (pmm) REVERT: A 360 ARG cc_start: 0.8762 (ptm160) cc_final: 0.8536 (ppp80) REVERT: A 480 ASN cc_start: 0.7722 (m-40) cc_final: 0.7500 (m-40) REVERT: A 731 PHE cc_start: 0.8108 (m-10) cc_final: 0.7544 (t80) REVERT: A 985 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 1023 MET cc_start: 0.7478 (mmp) cc_final: 0.6442 (ttp) REVERT: A 1059 MET cc_start: 0.8096 (mpp) cc_final: 0.7330 (pmm) REVERT: B 189 MET cc_start: 0.7666 (mpp) cc_final: 0.7390 (mtm) REVERT: B 194 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 353 MET cc_start: 0.7787 (mpp) cc_final: 0.7487 (pmm) REVERT: B 360 ARG cc_start: 0.8742 (ptm160) cc_final: 0.8514 (ppp80) REVERT: B 480 ASN cc_start: 0.7677 (m-40) cc_final: 0.7440 (m-40) REVERT: B 518 ASP cc_start: 0.8299 (t0) cc_final: 0.8055 (t0) REVERT: B 689 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7998 (p0) REVERT: B 731 PHE cc_start: 0.8113 (m-10) cc_final: 0.7559 (t80) REVERT: B 985 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 1001 LEU cc_start: 0.9147 (pp) cc_final: 0.8749 (tm) REVERT: B 1023 MET cc_start: 0.7485 (mmp) cc_final: 0.6435 (ttp) REVERT: B 1059 MET cc_start: 0.8091 (mpp) cc_final: 0.7305 (pmm) REVERT: C 189 MET cc_start: 0.7297 (mtm) cc_final: 0.6957 (mtt) REVERT: C 194 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8807 (mt-10) REVERT: C 353 MET cc_start: 0.7838 (mpp) cc_final: 0.7543 (pmm) REVERT: C 360 ARG cc_start: 0.8753 (ptm160) cc_final: 0.8523 (ppp80) REVERT: C 518 ASP cc_start: 0.8280 (t0) cc_final: 0.8033 (t0) REVERT: C 566 ILE cc_start: 0.9256 (mp) cc_final: 0.8988 (mp) REVERT: C 689 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8011 (p0) REVERT: C 731 PHE cc_start: 0.8072 (m-10) cc_final: 0.7518 (t80) REVERT: C 942 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: C 985 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 1001 LEU cc_start: 0.9145 (pp) cc_final: 0.8752 (tm) REVERT: C 1023 MET cc_start: 0.7478 (mmp) cc_final: 0.6424 (ttp) REVERT: C 1059 MET cc_start: 0.7950 (mpp) cc_final: 0.7424 (pmm) REVERT: D 189 MET cc_start: 0.7428 (mtm) cc_final: 0.7075 (mtt) REVERT: D 194 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8806 (mt-10) REVERT: D 353 MET cc_start: 0.7795 (mpp) cc_final: 0.7526 (pmm) REVERT: D 457 ASP cc_start: 0.7824 (t0) cc_final: 0.7474 (t0) REVERT: D 566 ILE cc_start: 0.9240 (mp) cc_final: 0.8981 (mp) REVERT: D 689 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8058 (p0) REVERT: D 731 PHE cc_start: 0.8088 (m-10) cc_final: 0.7553 (t80) REVERT: D 985 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 1001 LEU cc_start: 0.9141 (pp) cc_final: 0.8746 (tm) REVERT: D 1023 MET cc_start: 0.7480 (mmp) cc_final: 0.6422 (ttp) REVERT: D 1059 MET cc_start: 0.8102 (mpp) cc_final: 0.7327 (pmm) REVERT: D 1076 GLU cc_start: 0.8923 (pp20) cc_final: 0.8494 (pm20) outliers start: 65 outliers final: 41 residues processed: 411 average time/residue: 1.3175 time to fit residues: 648.3988 Evaluate side-chains 380 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 104 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 317 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 350 optimal weight: 4.9990 chunk 328 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 992 GLN B 992 GLN C 992 GLN D 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.123939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085631 restraints weight = 68419.894| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.83 r_work: 0.3186 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31192 Z= 0.170 Angle : 0.663 11.349 42260 Z= 0.345 Chirality : 0.042 0.153 4708 Planarity : 0.004 0.062 5280 Dihedral : 5.211 52.087 4024 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.07 % Allowed : 19.53 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3656 helix: 1.80 (0.10), residues: 2460 sheet: -1.63 (0.37), residues: 188 loop : -1.95 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 786 HIS 0.005 0.001 HIS B 138 PHE 0.043 0.002 PHE D1021 TYR 0.013 0.002 TYR D 186 ARG 0.012 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 1784) hydrogen bonds : angle 4.04902 ( 5292) SS BOND : bond 0.00689 ( 4) SS BOND : angle 4.45912 ( 8) covalent geometry : bond 0.00404 (31188) covalent geometry : angle 0.65995 (42252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33748.32 seconds wall clock time: 588 minutes 12.96 seconds (35292.96 seconds total)