Starting phenix.real_space_refine on Thu May 15 14:04:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.map" model { file = "/net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k98_36980/05_2025/8k98_36980.cif" } resolution = 2.9 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= 0.001 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8678 2.51 5 N 2147 2.21 5 O 2538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13415 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5812 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 687} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 890 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 5838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5838 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 688} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 7.43, per 1000 atoms: 0.55 Number of scatterers: 13415 At special positions: 0 Unit cell: (104.55, 121.55, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2538 8.00 N 2147 7.00 C 8678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 4 sheets defined 63.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 307 through 317 removed outlier: 4.253A pdb=" N TYR C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.520A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 322' Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 356 through 366 removed outlier: 4.286A pdb=" N PHE C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 361 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.950A pdb=" N LYS C 372 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.672A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.553A pdb=" N SER C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 495 removed outlier: 3.736A pdb=" N TYR C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.549A pdb=" N LEU C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.307A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 572 Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.996A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 639 Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 700 Processing helix chain 'C' and resid 705 through 723 removed outlier: 4.718A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 743 removed outlier: 3.532A pdb=" N TYR C 743 " --> pdb=" O ALA C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 761 removed outlier: 3.559A pdb=" N LEU C 761 " --> pdb=" O TRP C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.751A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.015A pdb=" N ILE C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.623A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 removed outlier: 3.838A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 880 through 903 removed outlier: 3.836A pdb=" N LEU C 884 " --> pdb=" O GLU C 880 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 893 " --> pdb=" O LEU C 889 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 902 " --> pdb=" O VAL C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 927 through 933 removed outlier: 4.485A pdb=" N PHE C 933 " --> pdb=" O MET C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 944 removed outlier: 4.053A pdb=" N PHE C 943 " --> pdb=" O GLN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 962 removed outlier: 4.624A pdb=" N LYS C 960 " --> pdb=" O PRO C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 975 through 990 removed outlier: 4.231A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1002 removed outlier: 3.689A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C1000 " --> pdb=" O TYR C 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.308A pdb=" N TYR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.944A pdb=" N LEU B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 356 through 366 removed outlier: 4.227A pdb=" N PHE B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.951A pdb=" N LYS B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.671A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 removed outlier: 3.545A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 494 removed outlier: 3.539A pdb=" N GLY B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.555A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.300A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.990A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.072A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.637A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.523A pdb=" N TYR B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.564A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 803 through 812 removed outlier: 3.704A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 825 removed outlier: 3.981A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.624A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.814A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 880 through 903 removed outlier: 3.844A pdb=" N LEU B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 893 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.539A pdb=" N LEU B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 939 No H-bonds generated for 'chain 'B' and resid 937 through 939' Processing helix chain 'B' and resid 940 through 945 Processing helix chain 'B' and resid 954 through 962 removed outlier: 4.697A pdb=" N LYS B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 975 through 990 removed outlier: 4.221A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1002 removed outlier: 3.632A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1000 " --> pdb=" O TYR B 996 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 15 removed outlier: 5.990A pdb=" N ARG A 15 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 21 " --> pdb=" O ARG A 15 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 63 current: chain 'A' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 191 through 195 current: chain 'A' and resid 219 through 222 Processing sheet with id=AA2, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 15 removed outlier: 6.684A pdb=" N VAL D 11 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR D 24 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE D 13 " --> pdb=" O VAL D 22 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'D' and resid 192 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 642 hydrogen bonds defined for protein. 1854 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: 3.73 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3001 1.33 - 1.45: 3186 1.45 - 1.57: 7431 1.57 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13706 Sorted by residual: bond pdb=" CA ARG A 15 " pdb=" C ARG A 15 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.28e-02 6.10e+03 3.08e+01 bond pdb=" N LYS A 16 " pdb=" CA LYS A 16 " ideal model delta sigma weight residual 1.457 1.402 0.055 1.29e-02 6.01e+03 1.84e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" CA SER C 855 " pdb=" C SER C 855 " ideal model delta sigma weight residual 1.525 1.485 0.041 1.29e-02 6.01e+03 9.86e+00 bond pdb=" CA LEU C 854 " pdb=" CB LEU C 854 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.53e-02 4.27e+03 8.68e+00 ... (remaining 13701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18264 2.43 - 4.85: 138 4.85 - 7.28: 18 7.28 - 9.71: 8 9.71 - 12.13: 3 Bond angle restraints: 18431 Sorted by residual: angle pdb=" N LYS A 16 " pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 110.80 98.67 12.13 2.13e+00 2.20e-01 3.25e+01 angle pdb=" N SER C 855 " pdb=" CA SER C 855 " pdb=" C SER C 855 " ideal model delta sigma weight residual 112.04 104.35 7.69 1.44e+00 4.82e-01 2.85e+01 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 110.44 104.81 5.63 1.20e+00 6.94e-01 2.20e+01 angle pdb=" CA GLU B 880 " pdb=" CB GLU B 880 " pdb=" CG GLU B 880 " ideal model delta sigma weight residual 114.10 122.37 -8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA GLU C 880 " pdb=" CB GLU C 880 " pdb=" CG GLU C 880 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 18426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6769 17.95 - 35.89: 993 35.89 - 53.84: 311 53.84 - 71.79: 59 71.79 - 89.73: 29 Dihedral angle restraints: 8161 sinusoidal: 3364 harmonic: 4797 Sorted by residual: dihedral pdb=" CA LYS B 953 " pdb=" C LYS B 953 " pdb=" N PHE B 954 " pdb=" CA PHE B 954 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LYS C 953 " pdb=" C LYS C 953 " pdb=" N PHE C 954 " pdb=" CA PHE C 954 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR B 906 " pdb=" C THR B 906 " pdb=" N PHE B 907 " pdb=" CA PHE B 907 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1617 0.053 - 0.106: 308 0.106 - 0.159: 28 0.159 - 0.212: 3 0.212 - 0.265: 4 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CG LEU B 959 " pdb=" CB LEU B 959 " pdb=" CD1 LEU B 959 " pdb=" CD2 LEU B 959 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU C 959 " pdb=" CB LEU C 959 " pdb=" CD1 LEU C 959 " pdb=" CD2 LEU C 959 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE B 515 " pdb=" CA ILE B 515 " pdb=" CG1 ILE B 515 " pdb=" CG2 ILE B 515 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1957 not shown) Planarity restraints: 2353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 878 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO C 879 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 879 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 879 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 343 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASN B 343 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN B 343 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 878 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 879 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 879 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 879 " 0.030 5.00e-02 4.00e+02 ... (remaining 2350 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 554 2.72 - 3.27: 13240 3.27 - 3.81: 21208 3.81 - 4.36: 25758 4.36 - 4.90: 44442 Nonbonded interactions: 105202 Sorted by model distance: nonbonded pdb=" OG SER C 429 " pdb=" OD1 ASP C 435 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 429 " pdb=" OD1 ASP B 435 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP D 225 " pdb=" OG1 THR D 228 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR C 709 " pdb=" OD2 ASP C 748 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 201 " pdb=" OG SER A 201 " model vdw 2.237 3.040 ... (remaining 105197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 33 or resid 52 through 177 or resid 190 through \ 211 or resid 216 through 236)) selection = (chain 'D' and (resid 5 through 74 or resid 168 through 227 or (resid 228 throug \ h 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thro \ ugh 235 or (resid 236 and (name N or name CA or name C or name O or name CB )))) \ } ncs_group { reference = (chain 'B' and (resid 304 through 638 or (resid 639 and (name N or name CA or na \ me C or name O or name CB )) or resid 640 or resid 643 through 932 or (resid 933 \ and (name N or name CA or name C or name O or name CB )) or resid 934 through 1 \ 005)) selection = (chain 'C' and (resid 304 through 349 or resid 354 through 1005)) } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.440 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13706 Z= 0.152 Angle : 0.581 12.134 18431 Z= 0.313 Chirality : 0.041 0.265 1960 Planarity : 0.003 0.057 2353 Dihedral : 19.216 89.734 5065 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.77 % Rotamer: Outliers : 3.15 % Allowed : 33.06 % Favored : 63.79 % 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: -0.15 (0.21), residues: 1589 helix: 0.73 (0.18), residues: 899 sheet: 1.25 (0.55), residues: 99 loop : -1.64 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 958 HIS 0.011 0.001 HIS C 349 PHE 0.031 0.001 PHE C 354 TYR 0.023 0.001 TYR B 356 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.15375 ( 642) hydrogen bonds : angle 5.47455 ( 1854) covalent geometry : bond 0.00283 (13706) covalent geometry : angle 0.58117 (18431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 1.472 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: B 320 PHE cc_start: 0.6420 (m-80) cc_final: 0.5455 (t80) REVERT: B 495 LEU cc_start: 0.6465 (tm) cc_final: 0.6261 (tp) outliers start: 46 outliers final: 40 residues processed: 213 average time/residue: 0.8757 time to fit residues: 211.1718 Evaluate side-chains 211 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 951 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN C 591 ASN ** C 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN B 349 HIS B 591 ASN B 606 HIS B 867 ASN B 910 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.224217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.194399 restraints weight = 16685.622| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.92 r_work: 0.4062 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13706 Z= 0.229 Angle : 0.641 8.685 18431 Z= 0.349 Chirality : 0.046 0.345 1960 Planarity : 0.004 0.054 2353 Dihedral : 7.305 58.895 1833 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 7.87 % Allowed : 27.31 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.79 (0.21), residues: 1589 helix: 0.20 (0.17), residues: 916 sheet: 0.74 (0.52), residues: 102 loop : -1.90 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 958 HIS 0.009 0.002 HIS B 349 PHE 0.023 0.002 PHE B 387 TYR 0.024 0.002 TYR B 472 ARG 0.003 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.05843 ( 642) hydrogen bonds : angle 4.64519 ( 1854) covalent geometry : bond 0.00536 (13706) covalent geometry : angle 0.64104 (18431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 178 time to evaluate : 1.394 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: C 730 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6096 (mt-10) REVERT: C 877 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: C 976 MET cc_start: 0.3590 (OUTLIER) cc_final: 0.2691 (ppp) REVERT: D 28 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: B 320 PHE cc_start: 0.6763 (m-80) cc_final: 0.6418 (m-80) REVERT: B 497 LEU cc_start: 0.7826 (mt) cc_final: 0.7619 (mt) REVERT: B 730 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5995 (mt-10) REVERT: B 760 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6864 (ptp-110) REVERT: B 877 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.4789 (m-80) REVERT: B 936 MET cc_start: 0.5353 (tmm) cc_final: 0.5121 (tmm) REVERT: B 976 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.2499 (ppp) outliers start: 115 outliers final: 41 residues processed: 271 average time/residue: 0.9091 time to fit residues: 278.5399 Evaluate side-chains 220 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 954 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 503 HIS ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.222099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.192497 restraints weight = 16746.165| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.88 r_work: 0.4044 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13706 Z= 0.238 Angle : 0.654 9.165 18431 Z= 0.355 Chirality : 0.046 0.347 1960 Planarity : 0.004 0.056 2353 Dihedral : 6.580 56.200 1789 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.95 % Rotamer: Outliers : 8.08 % Allowed : 28.47 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.07 (0.20), residues: 1589 helix: -0.05 (0.17), residues: 926 sheet: 0.41 (0.53), residues: 96 loop : -1.93 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 958 HIS 0.010 0.001 HIS C 349 PHE 0.025 0.002 PHE B 387 TYR 0.021 0.002 TYR C 472 ARG 0.003 0.000 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.05811 ( 642) hydrogen bonds : angle 4.68231 ( 1854) covalent geometry : bond 0.00563 (13706) covalent geometry : angle 0.65384 (18431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 184 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 626 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: C 730 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6047 (mt-10) REVERT: C 851 SER cc_start: 0.4650 (OUTLIER) cc_final: 0.4157 (m) REVERT: C 877 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.4659 (m-80) REVERT: C 900 LYS cc_start: 0.6291 (tppt) cc_final: 0.5910 (tptt) REVERT: C 976 MET cc_start: 0.3714 (OUTLIER) cc_final: 0.2733 (ppp) REVERT: C 1004 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4916 (t80) REVERT: D 28 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 320 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.5622 (t80) REVERT: B 629 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6572 (ptm160) REVERT: B 730 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5964 (mt-10) REVERT: B 760 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6926 (ptp-110) REVERT: B 877 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4999 (m-80) REVERT: B 936 MET cc_start: 0.5450 (tmm) cc_final: 0.4971 (tmm) REVERT: B 940 TYR cc_start: 0.5816 (t80) cc_final: 0.5556 (t80) REVERT: B 976 MET cc_start: 0.3745 (OUTLIER) cc_final: 0.2701 (ppp) outliers start: 118 outliers final: 48 residues processed: 280 average time/residue: 0.8613 time to fit residues: 272.4904 Evaluate side-chains 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 HIS C 349 HIS ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN B 339 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.221568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192092 restraints weight = 16669.004| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.86 r_work: 0.4037 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13706 Z= 0.255 Angle : 0.674 8.549 18431 Z= 0.366 Chirality : 0.046 0.377 1960 Planarity : 0.004 0.063 2353 Dihedral : 6.619 57.606 1787 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 8.83 % Allowed : 28.47 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.22 (0.20), residues: 1589 helix: -0.14 (0.17), residues: 921 sheet: 0.33 (0.53), residues: 96 loop : -2.04 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 958 HIS 0.010 0.002 HIS B 349 PHE 0.026 0.002 PHE B 387 TYR 0.024 0.003 TYR C 472 ARG 0.006 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05939 ( 642) hydrogen bonds : angle 4.75120 ( 1854) covalent geometry : bond 0.00607 (13706) covalent geometry : angle 0.67422 (18431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 187 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: C 320 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.5392 (t80) REVERT: C 535 PHE cc_start: 0.5778 (t80) cc_final: 0.5388 (t80) REVERT: C 626 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 730 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6035 (mt-10) REVERT: C 851 SER cc_start: 0.4543 (OUTLIER) cc_final: 0.3978 (m) REVERT: C 866 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6124 (mtp) REVERT: C 877 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: C 976 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3053 (ppp) REVERT: C 1004 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4972 (t80) REVERT: D 28 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: B 320 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.5674 (t80) REVERT: B 531 MET cc_start: 0.6966 (mtm) cc_final: 0.6689 (mtm) REVERT: B 629 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6602 (ptm160) REVERT: B 730 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5964 (mt-10) REVERT: B 760 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6868 (ptp-110) REVERT: B 851 SER cc_start: 0.4639 (OUTLIER) cc_final: 0.4040 (m) REVERT: B 866 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6108 (mtp) REVERT: B 877 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5115 (m-80) REVERT: B 976 MET cc_start: 0.3814 (OUTLIER) cc_final: 0.2903 (ppp) REVERT: B 998 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6497 (mt-10) REVERT: B 1004 PHE cc_start: 0.5477 (OUTLIER) cc_final: 0.4987 (t80) outliers start: 129 outliers final: 58 residues processed: 291 average time/residue: 0.8478 time to fit residues: 279.3943 Evaluate side-chains 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 181 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 636 PHE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.225530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196661 restraints weight = 16762.935| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.85 r_work: 0.4082 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13706 Z= 0.149 Angle : 0.586 8.380 18431 Z= 0.317 Chirality : 0.042 0.356 1960 Planarity : 0.004 0.056 2353 Dihedral : 5.867 57.560 1783 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.54 % Favored : 93.33 % Rotamer: Outliers : 5.61 % Allowed : 32.03 % Favored : 62.35 % 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 (0.21), residues: 1589 helix: 0.31 (0.17), residues: 919 sheet: 0.49 (0.53), residues: 98 loop : -1.92 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 601 HIS 0.010 0.001 HIS C 349 PHE 0.024 0.002 PHE C 354 TYR 0.020 0.002 TYR C 472 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 642) hydrogen bonds : angle 4.34895 ( 1854) covalent geometry : bond 0.00340 (13706) covalent geometry : angle 0.58623 (18431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 626 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: C 767 LEU cc_start: 0.7514 (tp) cc_final: 0.7058 (tt) REVERT: C 877 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.4550 (m-80) REVERT: C 907 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: C 1004 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4992 (t80) REVERT: D 28 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: B 320 PHE cc_start: 0.6724 (m-80) cc_final: 0.5709 (t80) REVERT: B 760 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6860 (ptp-110) REVERT: B 877 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.4924 (m-80) REVERT: B 930 MET cc_start: 0.6327 (mmm) cc_final: 0.6028 (mmm) REVERT: B 1004 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4984 (t80) outliers start: 82 outliers final: 30 residues processed: 246 average time/residue: 0.8768 time to fit residues: 243.8009 Evaluate side-chains 215 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 636 PHE Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN C 563 ASN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 867 ASN ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.220664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.191422 restraints weight = 16962.512| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.86 r_work: 0.4014 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13706 Z= 0.273 Angle : 0.702 8.698 18431 Z= 0.378 Chirality : 0.047 0.430 1960 Planarity : 0.004 0.057 2353 Dihedral : 6.070 59.757 1774 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.61 % Favored : 92.26 % Rotamer: Outliers : 8.28 % Allowed : 29.50 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.20 (0.20), residues: 1589 helix: -0.10 (0.17), residues: 915 sheet: 0.33 (0.53), residues: 98 loop : -2.08 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 958 HIS 0.013 0.002 HIS C 978 PHE 0.027 0.003 PHE C 943 TYR 0.028 0.003 TYR C 472 ARG 0.003 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.06064 ( 642) hydrogen bonds : angle 4.75043 ( 1854) covalent geometry : bond 0.00648 (13706) covalent geometry : angle 0.70187 (18431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 183 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: C 320 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.5440 (t80) REVERT: C 535 PHE cc_start: 0.5778 (t80) cc_final: 0.5472 (t80) REVERT: C 626 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 730 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6112 (mt-10) REVERT: C 851 SER cc_start: 0.4560 (OUTLIER) cc_final: 0.4008 (m) REVERT: C 877 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: C 907 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: C 1004 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.5089 (t80) REVERT: D 28 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: B 320 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.5583 (t80) REVERT: B 730 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6005 (mt-10) REVERT: B 760 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6749 (ptp-110) REVERT: B 851 SER cc_start: 0.4627 (OUTLIER) cc_final: 0.4047 (m) REVERT: B 877 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5144 (m-80) REVERT: B 938 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 998 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6424 (mt-10) REVERT: B 1004 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4976 (t80) outliers start: 121 outliers final: 53 residues processed: 279 average time/residue: 0.8208 time to fit residues: 260.4101 Evaluate side-chains 246 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 765 ASN C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS B 867 ASN B 978 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.226405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197598 restraints weight = 16775.454| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.86 r_work: 0.4083 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13706 Z= 0.131 Angle : 0.592 10.184 18431 Z= 0.318 Chirality : 0.042 0.371 1960 Planarity : 0.004 0.059 2353 Dihedral : 5.435 53.961 1774 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 4.86 % Allowed : 32.72 % Favored : 62.42 % 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: -0.67 (0.21), residues: 1589 helix: 0.39 (0.17), residues: 921 sheet: 0.51 (0.54), residues: 98 loop : -2.00 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 958 HIS 0.018 0.002 HIS C 978 PHE 0.021 0.001 PHE B 387 TYR 0.019 0.002 TYR C 472 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 642) hydrogen bonds : angle 4.27415 ( 1854) covalent geometry : bond 0.00291 (13706) covalent geometry : angle 0.59157 (18431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 178 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 PHE cc_start: 0.6759 (m-80) cc_final: 0.5474 (t80) REVERT: C 772 ILE cc_start: 0.7604 (mt) cc_final: 0.7350 (mp) REVERT: C 877 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.4694 (m-80) REVERT: C 995 ARG cc_start: 0.7254 (tpt170) cc_final: 0.7003 (tpt170) REVERT: C 1004 PHE cc_start: 0.5300 (OUTLIER) cc_final: 0.5002 (t80) REVERT: D 28 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: B 320 PHE cc_start: 0.6795 (m-80) cc_final: 0.5796 (t80) REVERT: B 531 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6319 (mtp) REVERT: B 760 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6789 (ptp-110) REVERT: B 851 SER cc_start: 0.4453 (OUTLIER) cc_final: 0.4033 (m) REVERT: B 877 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5088 (m-80) REVERT: B 1004 PHE cc_start: 0.5356 (OUTLIER) cc_final: 0.4984 (t80) outliers start: 71 outliers final: 36 residues processed: 236 average time/residue: 0.8651 time to fit residues: 230.8157 Evaluate side-chains 218 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 0.0040 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.225641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196675 restraints weight = 16824.256| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.86 r_work: 0.4081 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13706 Z= 0.154 Angle : 0.611 11.906 18431 Z= 0.325 Chirality : 0.043 0.427 1960 Planarity : 0.004 0.057 2353 Dihedral : 5.370 51.168 1774 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.05 % Favored : 92.83 % Rotamer: Outliers : 4.86 % Allowed : 32.65 % Favored : 62.49 % 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: -0.63 (0.21), residues: 1589 helix: 0.43 (0.17), residues: 921 sheet: 0.51 (0.54), residues: 98 loop : -1.97 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 601 HIS 0.016 0.002 HIS C 978 PHE 0.023 0.002 PHE B 387 TYR 0.021 0.002 TYR C 472 ARG 0.004 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 642) hydrogen bonds : angle 4.28029 ( 1854) covalent geometry : bond 0.00356 (13706) covalent geometry : angle 0.61064 (18431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 PHE cc_start: 0.6725 (m-80) cc_final: 0.5450 (t80) REVERT: C 357 MET cc_start: 0.7381 (mpt) cc_final: 0.6727 (mpp) REVERT: C 535 PHE cc_start: 0.5549 (t80) cc_final: 0.5199 (t80) REVERT: C 767 LEU cc_start: 0.7458 (tp) cc_final: 0.7042 (tt) REVERT: C 877 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: C 995 ARG cc_start: 0.7293 (tpt170) cc_final: 0.7029 (tpt170) REVERT: C 1004 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4954 (t80) REVERT: D 28 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: B 320 PHE cc_start: 0.6785 (m-80) cc_final: 0.5634 (t80) REVERT: B 349 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6525 (t-90) REVERT: B 639 PHE cc_start: 0.4286 (OUTLIER) cc_final: 0.4023 (t80) REVERT: B 760 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6787 (ptp-110) REVERT: B 851 SER cc_start: 0.4477 (OUTLIER) cc_final: 0.4040 (m) REVERT: B 877 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5052 (m-80) REVERT: B 930 MET cc_start: 0.6304 (mmm) cc_final: 0.5959 (mmm) REVERT: B 940 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: B 1004 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.5007 (t80) outliers start: 71 outliers final: 42 residues processed: 239 average time/residue: 0.8802 time to fit residues: 239.3736 Evaluate side-chains 232 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 639 PHE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.222263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.193079 restraints weight = 16761.916| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.85 r_work: 0.4049 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13706 Z= 0.239 Angle : 0.683 11.417 18431 Z= 0.365 Chirality : 0.046 0.475 1960 Planarity : 0.004 0.058 2353 Dihedral : 5.727 54.019 1772 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 5.13 % Allowed : 32.38 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.00 (0.21), residues: 1589 helix: 0.10 (0.17), residues: 917 sheet: 0.37 (0.54), residues: 98 loop : -2.07 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 958 HIS 0.018 0.002 HIS C 978 PHE 0.024 0.002 PHE B 387 TYR 0.027 0.002 TYR C 472 ARG 0.005 0.001 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 642) hydrogen bonds : angle 4.56725 ( 1854) covalent geometry : bond 0.00571 (13706) covalent geometry : angle 0.68307 (18431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: C 320 PHE cc_start: 0.6808 (m-80) cc_final: 0.5527 (t80) REVERT: C 349 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.6247 (t-90) REVERT: C 357 MET cc_start: 0.7490 (mpt) cc_final: 0.6744 (mpp) REVERT: C 535 PHE cc_start: 0.5641 (t80) cc_final: 0.5250 (t80) REVERT: C 840 LYS cc_start: 0.5477 (mmtt) cc_final: 0.4997 (mmmt) REVERT: C 851 SER cc_start: 0.4501 (OUTLIER) cc_final: 0.4048 (m) REVERT: C 877 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.4982 (m-80) REVERT: C 995 ARG cc_start: 0.7318 (tpt170) cc_final: 0.7069 (tpt170) REVERT: C 1004 PHE cc_start: 0.5270 (OUTLIER) cc_final: 0.4989 (t80) REVERT: D 28 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: B 320 PHE cc_start: 0.6831 (m-80) cc_final: 0.5609 (t80) REVERT: B 639 PHE cc_start: 0.4449 (OUTLIER) cc_final: 0.4093 (t80) REVERT: B 760 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6705 (ptp-110) REVERT: B 851 SER cc_start: 0.4585 (OUTLIER) cc_final: 0.4049 (m) REVERT: B 877 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: B 1004 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4977 (t80) outliers start: 75 outliers final: 46 residues processed: 242 average time/residue: 0.8507 time to fit residues: 233.1858 Evaluate side-chains 233 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 639 PHE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 155 optimal weight: 0.0010 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 978 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.226358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.197479 restraints weight = 16798.304| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.86 r_work: 0.4082 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13706 Z= 0.135 Angle : 0.615 12.334 18431 Z= 0.327 Chirality : 0.042 0.408 1960 Planarity : 0.004 0.058 2353 Dihedral : 5.293 48.956 1772 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.27 % Rotamer: Outliers : 3.83 % Allowed : 33.47 % Favored : 62.70 % 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: -0.58 (0.21), residues: 1589 helix: 0.50 (0.17), residues: 920 sheet: 0.52 (0.55), residues: 98 loop : -2.01 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 958 HIS 0.019 0.002 HIS C 978 PHE 0.022 0.001 PHE B 387 TYR 0.018 0.002 TYR C 472 ARG 0.011 0.000 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 642) hydrogen bonds : angle 4.27079 ( 1854) covalent geometry : bond 0.00305 (13706) covalent geometry : angle 0.61522 (18431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 PHE cc_start: 0.6848 (m-80) cc_final: 0.5575 (t80) REVERT: C 357 MET cc_start: 0.7471 (mpt) cc_final: 0.6746 (mpp) REVERT: C 535 PHE cc_start: 0.5540 (t80) cc_final: 0.5161 (t80) REVERT: C 772 ILE cc_start: 0.7633 (mt) cc_final: 0.7368 (mp) REVERT: C 877 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: C 995 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6995 (tpt170) REVERT: C 1004 PHE cc_start: 0.5219 (OUTLIER) cc_final: 0.4912 (t80) REVERT: B 320 PHE cc_start: 0.6768 (m-80) cc_final: 0.5611 (t80) REVERT: B 639 PHE cc_start: 0.4396 (OUTLIER) cc_final: 0.4082 (t80) REVERT: B 760 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6807 (ptp-110) REVERT: B 851 SER cc_start: 0.4448 (OUTLIER) cc_final: 0.4046 (m) REVERT: B 877 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: B 930 MET cc_start: 0.6432 (mmm) cc_final: 0.6140 (mmm) REVERT: B 1004 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.5058 (t80) outliers start: 56 outliers final: 36 residues processed: 227 average time/residue: 0.8774 time to fit residues: 225.1827 Evaluate side-chains 215 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 639 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1004 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.225484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.196492 restraints weight = 16723.573| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.86 r_work: 0.4074 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13706 Z= 0.167 Angle : 0.640 12.527 18431 Z= 0.338 Chirality : 0.043 0.441 1960 Planarity : 0.004 0.057 2353 Dihedral : 5.323 47.433 1772 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 3.63 % Allowed : 33.88 % Favored : 62.49 % 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: -0.65 (0.21), residues: 1589 helix: 0.41 (0.17), residues: 921 sheet: 0.51 (0.55), residues: 98 loop : -1.98 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 601 HIS 0.015 0.002 HIS C 978 PHE 0.031 0.002 PHE C 354 TYR 0.021 0.002 TYR C 472 ARG 0.005 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 642) hydrogen bonds : angle 4.34559 ( 1854) covalent geometry : bond 0.00390 (13706) covalent geometry : angle 0.64004 (18431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9259.95 seconds wall clock time: 160 minutes 6.44 seconds (9606.44 seconds total)