Starting phenix.real_space_refine on Sat Oct 11 08:37:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k98_36980/10_2025/8k98_36980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k98_36980/10_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_36980/10_2025/8k98_36980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k98_36980/10_2025/8k98_36980.map" model { file = "/net/cci-nas-00/data/ceres_data/8k98_36980/10_2025/8k98_36980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k98_36980/10_2025/8k98_36980.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.111 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'GLU: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: {'ASP:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.12, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 530.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 1.89 Time building geometry restraints manager: 1.41 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: 1.060 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (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 ARG 0.002 0.000 ARG A 170 TYR 0.023 0.001 TYR B 356 PHE 0.031 0.001 PHE C 354 TRP 0.009 0.001 TRP C 958 HIS 0.011 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00283 (13706) covalent geometry : angle 0.58117 (18431) hydrogen bonds : bond 0.15375 ( 642) hydrogen bonds : angle 5.47455 ( 1854) *********************** 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 : 0.474 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: 0.4184 time to fit residues: 100.6020 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 : 0.475 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4472 r_free = 0.4472 target = 0.225758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.195831 restraints weight = 16709.767| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.91 r_work: 0.4077 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13706 Z= 0.197 Angle : 0.610 8.545 18431 Z= 0.332 Chirality : 0.044 0.336 1960 Planarity : 0.004 0.053 2353 Dihedral : 7.098 58.923 1833 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 7.60 % Allowed : 26.97 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.21), residues: 1589 helix: 0.38 (0.17), residues: 910 sheet: 0.82 (0.52), residues: 102 loop : -1.82 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 629 TYR 0.022 0.002 TYR B 472 PHE 0.023 0.002 PHE B 387 TRP 0.007 0.002 TRP C 958 HIS 0.009 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00456 (13706) covalent geometry : angle 0.61008 (18431) hydrogen bonds : bond 0.05239 ( 642) hydrogen bonds : angle 4.49514 ( 1854) *********************** 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: 111 poor density : 182 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 730 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6030 (mt-10) REVERT: C 767 LEU cc_start: 0.7663 (tp) cc_final: 0.7090 (tt) REVERT: C 877 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: C 938 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6184 (p0) REVERT: C 976 MET cc_start: 0.3459 (OUTLIER) cc_final: 0.2603 (ppp) REVERT: D 28 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: B 497 LEU cc_start: 0.7805 (mt) cc_final: 0.7595 (mt) REVERT: B 730 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: B 760 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6825 (ptp-110) REVERT: B 877 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: B 936 MET cc_start: 0.5242 (tmm) cc_final: 0.4968 (tmm) REVERT: B 976 MET cc_start: 0.3360 (OUTLIER) cc_final: 0.2428 (ppp) outliers start: 111 outliers final: 37 residues processed: 271 average time/residue: 0.4051 time to fit residues: 124.0885 Evaluate side-chains 224 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 938 ASP 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 567 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 848 ASN 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 933 PHE Chi-restraints excluded: chain B residue 940 TYR 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 115 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS B 349 HIS B 467 ASN B 797 ASN B 852 HIS B 910 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.230760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.202203 restraints weight = 16848.395| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.84 r_work: 0.4137 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4026 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13706 Z= 0.107 Angle : 0.525 8.856 18431 Z= 0.283 Chirality : 0.040 0.312 1960 Planarity : 0.003 0.054 2353 Dihedral : 5.228 58.287 1783 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 4.24 % Allowed : 30.12 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1589 helix: 0.74 (0.17), residues: 919 sheet: 1.02 (0.56), residues: 97 loop : -1.60 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 760 TYR 0.014 0.001 TYR B 951 PHE 0.023 0.001 PHE B 387 TRP 0.006 0.001 TRP B 601 HIS 0.009 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00224 (13706) covalent geometry : angle 0.52510 (18431) hydrogen bonds : bond 0.03759 ( 642) hydrogen bonds : angle 4.05369 ( 1854) *********************** 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 250 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 LEU cc_start: 0.6464 (mp) cc_final: 0.6230 (mp) REVERT: C 767 LEU cc_start: 0.7414 (tp) cc_final: 0.6834 (tt) REVERT: C 877 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.4682 (m-80) REVERT: C 900 LYS cc_start: 0.5929 (tppt) cc_final: 0.5609 (tptt) REVERT: C 907 PHE cc_start: 0.6621 (m-80) cc_final: 0.6221 (t80) REVERT: C 936 MET cc_start: 0.5461 (mpp) cc_final: 0.4650 (tmt) REVERT: B 760 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6837 (ptp-110) REVERT: B 877 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.4684 (m-80) REVERT: B 930 MET cc_start: 0.6331 (mmm) cc_final: 0.5994 (mmm) REVERT: B 936 MET cc_start: 0.5575 (tmm) cc_final: 0.5243 (tmm) outliers start: 62 outliers final: 17 residues processed: 236 average time/residue: 0.4515 time to fit residues: 119.4954 Evaluate side-chains 190 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 877 PHE 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 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 707 VAL 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 921 PHE Chi-restraints excluded: chain B residue 940 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 159 optimal weight: 0.0060 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 153 optimal weight: 0.0370 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 0.0070 overall best weight: 0.7894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS B 349 HIS B 467 ASN B 475 GLN B 797 ASN B 867 ASN B 910 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.231761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.202973 restraints weight = 16841.363| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 1.85 r_work: 0.4197 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4088 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13706 Z= 0.106 Angle : 0.516 10.243 18431 Z= 0.277 Chirality : 0.040 0.338 1960 Planarity : 0.003 0.054 2353 Dihedral : 4.665 52.095 1771 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 4.72 % Allowed : 30.25 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1589 helix: 0.87 (0.17), residues: 920 sheet: 1.02 (0.55), residues: 99 loop : -1.57 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.017 0.001 TYR B 539 PHE 0.023 0.001 PHE B 387 TRP 0.006 0.001 TRP B 601 HIS 0.010 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00226 (13706) covalent geometry : angle 0.51628 (18431) hydrogen bonds : bond 0.03537 ( 642) hydrogen bonds : angle 3.93173 ( 1854) *********************** 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 253 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 0.394 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 319 LEU cc_start: 0.6494 (mp) cc_final: 0.6229 (mp) REVERT: C 767 LEU cc_start: 0.7350 (tp) cc_final: 0.6806 (tt) REVERT: C 877 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.4544 (m-80) REVERT: C 907 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.6214 (t80) REVERT: C 936 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4501 (tmt) REVERT: B 554 ASP cc_start: 0.8268 (m-30) cc_final: 0.8002 (m-30) REVERT: B 760 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6703 (ptp-110) REVERT: B 877 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.4610 (m-80) outliers start: 69 outliers final: 25 residues processed: 238 average time/residue: 0.4137 time to fit residues: 110.9108 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 907 PHE Chi-restraints excluded: chain C residue 936 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 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 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 639 PHE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 797 ASN 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 921 PHE Chi-restraints excluded: chain B residue 940 TYR 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 3 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 867 ASN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** 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 = 0.4447 r_free = 0.4447 target = 0.222988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192999 restraints weight = 16878.784| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.96 r_work: 0.4051 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13706 Z= 0.256 Angle : 0.674 8.536 18431 Z= 0.362 Chirality : 0.047 0.411 1960 Planarity : 0.004 0.066 2353 Dihedral : 5.481 59.753 1771 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 6.91 % Allowed : 28.82 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.20), residues: 1589 helix: 0.23 (0.17), residues: 909 sheet: 0.74 (0.52), residues: 101 loop : -1.89 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 348 TYR 0.027 0.002 TYR C 472 PHE 0.027 0.002 PHE C 943 TRP 0.013 0.002 TRP C 958 HIS 0.010 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00609 (13706) covalent geometry : angle 0.67415 (18431) hydrogen bonds : bond 0.05848 ( 642) hydrogen bonds : angle 4.55136 ( 1854) *********************** 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 290 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 189 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6350 (t-90) REVERT: C 730 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5980 (mt-10) REVERT: C 851 SER cc_start: 0.4578 (OUTLIER) cc_final: 0.4160 (m) REVERT: C 877 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.4684 (m-80) REVERT: C 1004 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.4976 (t80) REVERT: D 28 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: B 531 MET cc_start: 0.6914 (mtm) cc_final: 0.6624 (mtm) REVERT: B 629 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6584 (ptm160) REVERT: B 730 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5992 (mt-10) REVERT: B 760 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6816 (ptp-110) REVERT: B 877 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.4924 (m-80) REVERT: B 1004 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.5102 (t80) outliers start: 101 outliers final: 50 residues processed: 272 average time/residue: 0.4307 time to fit residues: 131.6230 Evaluate side-chains 238 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 70 LEU 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 349 HIS Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 715 GLU 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 921 PHE Chi-restraints excluded: chain C residue 959 LEU 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 319 LEU 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 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 588 LEU 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 715 GLU 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 771 ILE 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 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 940 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 31 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.227131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.197906 restraints weight = 16741.562| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.91 r_work: 0.4094 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13706 Z= 0.138 Angle : 0.573 9.118 18431 Z= 0.308 Chirality : 0.042 0.366 1960 Planarity : 0.004 0.055 2353 Dihedral : 4.978 57.987 1768 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 5.07 % Allowed : 31.49 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1589 helix: 0.57 (0.17), residues: 908 sheet: 0.62 (0.55), residues: 96 loop : -1.79 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 176 TYR 0.018 0.002 TYR C 356 PHE 0.024 0.001 PHE B 387 TRP 0.006 0.001 TRP B 958 HIS 0.015 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00310 (13706) covalent geometry : angle 0.57269 (18431) hydrogen bonds : bond 0.04358 ( 642) hydrogen bonds : angle 4.20265 ( 1854) *********************** 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 253 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 730 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: C 767 LEU cc_start: 0.7416 (tp) cc_final: 0.6961 (tt) REVERT: C 877 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.4602 (m-80) REVERT: C 913 MET cc_start: 0.7355 (ttt) cc_final: 0.7116 (ttt) REVERT: D 26 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: B 349 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6341 (t-90) REVERT: B 730 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5856 (mt-10) REVERT: B 760 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6834 (ptp-110) REVERT: B 877 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.4759 (m-80) outliers start: 74 outliers final: 32 residues processed: 235 average time/residue: 0.4448 time to fit residues: 117.0001 Evaluate side-chains 209 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU 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 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU 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 339 HIS Chi-restraints excluded: chain B residue 345 THR 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 567 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 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 921 PHE Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 113 optimal weight: 0.0870 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 475 GLN B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.226075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196743 restraints weight = 16744.332| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.91 r_work: 0.4091 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13706 Z= 0.154 Angle : 0.596 10.874 18431 Z= 0.318 Chirality : 0.043 0.404 1960 Planarity : 0.004 0.056 2353 Dihedral : 4.957 55.666 1768 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 5.13 % Allowed : 31.49 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1589 helix: 0.59 (0.17), residues: 908 sheet: 0.63 (0.54), residues: 98 loop : -1.85 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.018 0.002 TYR C 356 PHE 0.024 0.002 PHE B 387 TRP 0.006 0.001 TRP C 601 HIS 0.003 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00355 (13706) covalent geometry : angle 0.59584 (18431) hydrogen bonds : bond 0.04422 ( 642) hydrogen bonds : angle 4.20674 ( 1854) *********************** 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 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 PHE cc_start: 0.6814 (m-80) cc_final: 0.6573 (m-80) REVERT: C 730 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5933 (mt-10) REVERT: C 767 LEU cc_start: 0.7400 (tp) cc_final: 0.6948 (tt) REVERT: C 877 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.4675 (m-80) REVERT: C 938 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5918 (p0) REVERT: D 26 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 320 PHE cc_start: 0.6652 (m-80) cc_final: 0.6416 (m-80) REVERT: B 531 MET cc_start: 0.6997 (mtm) cc_final: 0.6751 (mtm) REVERT: B 629 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6490 (ptm160) REVERT: B 730 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5873 (mt-10) REVERT: B 760 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6802 (ptp-110) REVERT: B 877 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.4759 (m-80) outliers start: 75 outliers final: 44 residues processed: 237 average time/residue: 0.4368 time to fit residues: 116.0836 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 636 PHE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 730 GLU 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 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU 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 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR 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 567 SER Chi-restraints excluded: chain B residue 573 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 760 ARG Chi-restraints excluded: chain B residue 796 SER 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 887 GLU Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 141 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.229996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201073 restraints weight = 16737.722| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.88 r_work: 0.4122 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13706 Z= 0.113 Angle : 0.565 12.179 18431 Z= 0.298 Chirality : 0.042 0.396 1960 Planarity : 0.003 0.056 2353 Dihedral : 4.640 46.913 1768 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 3.83 % Allowed : 32.92 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1589 helix: 0.86 (0.17), residues: 914 sheet: 0.79 (0.57), residues: 96 loop : -1.70 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.017 0.001 TYR C 356 PHE 0.029 0.001 PHE C 354 TRP 0.008 0.001 TRP C 601 HIS 0.002 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00245 (13706) covalent geometry : angle 0.56459 (18431) hydrogen bonds : bond 0.03563 ( 642) hydrogen bonds : angle 3.96680 ( 1854) *********************** 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 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7753 (tmm-80) REVERT: C 767 LEU cc_start: 0.7283 (tp) cc_final: 0.6825 (tt) REVERT: C 877 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.4609 (m-80) REVERT: D 26 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: B 320 PHE cc_start: 0.6609 (m-80) cc_final: 0.5486 (t80) REVERT: B 629 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6373 (ptm160) REVERT: B 730 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5750 (mt-10) REVERT: B 760 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6653 (ptp-110) REVERT: B 877 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: B 976 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.3031 (pmt) outliers start: 56 outliers final: 24 residues processed: 230 average time/residue: 0.4226 time to fit residues: 108.7793 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 308 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 877 PHE 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 D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 339 HIS 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 570 SER Chi-restraints excluded: chain B residue 629 ARG 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 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 135 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 ASN B 910 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.231620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.203098 restraints weight = 16924.247| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.85 r_work: 0.4141 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13706 Z= 0.109 Angle : 0.569 12.734 18431 Z= 0.298 Chirality : 0.041 0.389 1960 Planarity : 0.003 0.057 2353 Dihedral : 4.441 38.967 1768 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 2.74 % Allowed : 34.09 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1589 helix: 1.02 (0.18), residues: 913 sheet: 0.87 (0.56), residues: 98 loop : -1.65 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 176 TYR 0.023 0.001 TYR C 356 PHE 0.024 0.001 PHE B 387 TRP 0.009 0.001 TRP C 601 HIS 0.002 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00237 (13706) covalent geometry : angle 0.56864 (18431) hydrogen bonds : bond 0.03307 ( 642) hydrogen bonds : angle 3.86503 ( 1854) *********************** 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 225 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7747 (tmm-80) REVERT: C 319 LEU cc_start: 0.6329 (mp) cc_final: 0.6069 (mp) REVERT: C 343 ASN cc_start: 0.7086 (p0) cc_final: 0.6146 (t0) REVERT: C 767 LEU cc_start: 0.7235 (tp) cc_final: 0.6786 (tt) REVERT: C 877 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4649 (m-80) REVERT: D 26 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: B 320 PHE cc_start: 0.6610 (m-80) cc_final: 0.5588 (t80) REVERT: B 425 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5625 (mm) REVERT: B 730 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: B 760 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6655 (ptp-110) REVERT: B 877 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.4768 (m-80) outliers start: 40 outliers final: 22 residues processed: 215 average time/residue: 0.4338 time to fit residues: 104.7991 Evaluate side-chains 209 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR 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 567 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 730 GLU 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 887 GLU Chi-restraints excluded: chain B residue 940 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.225098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195094 restraints weight = 16878.035| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.01 r_work: 0.4079 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13706 Z= 0.210 Angle : 0.655 11.646 18431 Z= 0.346 Chirality : 0.045 0.451 1960 Planarity : 0.004 0.053 2353 Dihedral : 4.954 46.985 1767 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 2.74 % Allowed : 34.09 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1589 helix: 0.64 (0.17), residues: 909 sheet: 0.57 (0.55), residues: 98 loop : -1.79 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 176 TYR 0.025 0.002 TYR B 962 PHE 0.028 0.002 PHE C 354 TRP 0.011 0.002 TRP C 958 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00496 (13706) covalent geometry : angle 0.65544 (18431) hydrogen bonds : bond 0.04899 ( 642) hydrogen bonds : angle 4.24494 ( 1854) ********************** 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 221 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 772 ILE cc_start: 0.7716 (mt) cc_final: 0.7432 (mp) REVERT: C 840 LYS cc_start: 0.5467 (mmtt) cc_final: 0.4879 (mmmt) REVERT: C 877 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.4694 (m-80) REVERT: D 26 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: B 320 PHE cc_start: 0.6731 (m-80) cc_final: 0.5623 (t80) REVERT: B 425 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5943 (mm) REVERT: B 730 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5917 (mt-10) REVERT: B 760 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6633 (ptp-110) REVERT: B 877 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: B 976 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.3125 (pmt) outliers start: 40 outliers final: 26 residues processed: 213 average time/residue: 0.4714 time to fit residues: 112.8062 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 877 PHE 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 D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR 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 567 SER Chi-restraints excluded: chain B residue 570 SER 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 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 0.9990 chunk 79 optimal weight: 0.0030 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.230302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201508 restraints weight = 16989.955| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.84 r_work: 0.4134 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13706 Z= 0.114 Angle : 0.592 12.640 18431 Z= 0.310 Chirality : 0.041 0.382 1960 Planarity : 0.003 0.057 2353 Dihedral : 4.558 38.533 1767 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 2.26 % Allowed : 34.43 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.21), residues: 1589 helix: 0.95 (0.18), residues: 910 sheet: 0.69 (0.56), residues: 98 loop : -1.67 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 176 TYR 0.023 0.002 TYR B 962 PHE 0.032 0.001 PHE C 354 TRP 0.008 0.001 TRP B 601 HIS 0.002 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00248 (13706) covalent geometry : angle 0.59200 (18431) hydrogen bonds : bond 0.03540 ( 642) hydrogen bonds : angle 3.98404 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.51 seconds wall clock time: 79 minutes 33.18 seconds (4773.18 seconds total)