Starting phenix.real_space_refine on Sun Aug 24 22:08:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.map" model { file = "/net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f3e_28848/08_2025/8f3e_28848.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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 132 5.16 5 C 15094 2.51 5 N 3981 2.21 5 O 4420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23627 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7871 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 7876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7876 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 7880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7880 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.12, per 1000 atoms: 0.22 Number of scatterers: 23627 At special positions: 0 Unit cell: (123.05, 116.63, 142.31, 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 132 16.00 O 4420 8.00 N 3981 7.00 C 15094 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 23 sheets defined 59.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.644A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.575A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.503A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.946A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.581A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.515A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.639A pdb=" N GLN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 386 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.327A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.536A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.655A pdb=" N PHE A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 496 removed outlier: 3.548A pdb=" N GLY A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.448A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 869 through 891 removed outlier: 3.936A pdb=" N ALA A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.874A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 917 removed outlier: 3.881A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 Processing helix chain 'A' and resid 957 through 988 removed outlier: 4.687A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.502A pdb=" N ILE A1016 " --> pdb=" O THR A1012 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.627A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.576A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.759A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.723A pdb=" N VAL B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.787A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.840A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.761A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.713A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 460 through 496 removed outlier: 3.550A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.767A pdb=" N HIS B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 557 removed outlier: 3.727A pdb=" N ILE B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 775 through 778 Processing helix chain 'B' and resid 780 through 786 removed outlier: 3.737A pdb=" N ILE B 784 " --> pdb=" O PRO B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 847 removed outlier: 3.511A pdb=" N LYS B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 894 through 901 Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.544A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 3.780A pdb=" N THR B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 968 Processing helix chain 'B' and resid 968 through 988 Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1014 removed outlier: 3.503A pdb=" N GLN B 997 " --> pdb=" O GLY B 993 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B1013 " --> pdb=" O ILE B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1030 Proline residue: B1020 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.529A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 99 through 115 removed outlier: 4.211A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.501A pdb=" N VAL C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.608A pdb=" N PHE C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.557A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 3.923A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.588A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 5.673A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.830A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 496 removed outlier: 4.620A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 534 removed outlier: 3.596A pdb=" N LEU C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 558 Processing helix chain 'C' and resid 582 through 598 Processing helix chain 'C' and resid 642 through 655 Processing helix chain 'C' and resid 690 through 708 removed outlier: 3.772A pdb=" N GLU C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 752 removed outlier: 3.541A pdb=" N ALA C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 779 removed outlier: 4.262A pdb=" N MET C 779 " --> pdb=" O PRO C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 786 removed outlier: 3.934A pdb=" N ILE C 784 " --> pdb=" O PRO C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 847 removed outlier: 3.827A pdb=" N LYS C 847 " --> pdb=" O GLU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.511A pdb=" N GLN C 863 " --> pdb=" O ALA C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 891 Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 902 through 917 removed outlier: 3.799A pdb=" N GLY C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 953 removed outlier: 3.783A pdb=" N LEU C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 988 removed outlier: 4.935A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Proline residue: C 971 - end of helix Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 993 through 1030 removed outlier: 4.462A pdb=" N GLY C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Proline residue: C1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.137A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.597A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 824 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS A 716 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 826 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 714 " --> pdb=" O VAL A 826 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.137A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.597A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.485A pdb=" N SER A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.436A pdb=" N SER A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 612 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 629 " --> pdb=" O MET A 606 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A 608 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 627 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 610 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A 625 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 612 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 623 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.761A pdb=" N TYR A 182 " --> pdb=" O LYS A 768 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N TYR A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET A 184 " --> pdb=" O TYR A 770 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 772 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE A 186 " --> pdb=" O GLN A 772 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.369A pdb=" N THR A 233 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 727 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN A 235 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE B 729 " --> pdb=" O ASN A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'A' and resid 803 through 810 removed outlier: 8.627A pdb=" N ASN C 235 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 725 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.166A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 77 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 12.428A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.166A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 77 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 12.428A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER B 821 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.614A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.422A pdb=" N TYR B 182 " --> pdb=" O LYS B 768 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET B 184 " --> pdb=" O TYR B 770 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN B 772 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE B 186 " --> pdb=" O GLN B 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.885A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 233 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AB7, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.892A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 77 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU C 828 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG C 713 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.892A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 77 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 821 " --> pdb=" O ASP C 685 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.505A pdb=" N SER C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 138 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.577A pdb=" N ALA C 286 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.839A pdb=" N TYR C 182 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS C 768 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN C 758 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 771 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR C 756 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.617A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 788 through 790 1628 hydrogen bonds defined for protein. 4743 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: 4.90 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7749 1.34 - 1.46: 3241 1.46 - 1.57: 12838 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 24080 Sorted by residual: bond pdb=" CA ASN B 921 " pdb=" C ASN B 921 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.11e-02 8.12e+03 3.82e+00 bond pdb=" CA LEU C 874 " pdb=" C LEU C 874 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.27e-02 6.20e+03 2.66e+00 bond pdb=" CA ASP B 922 " pdb=" C ASP B 922 " ideal model delta sigma weight residual 1.528 1.508 0.021 1.28e-02 6.10e+03 2.63e+00 bond pdb=" CA ILE B 466 " pdb=" C ILE B 466 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.22e-02 6.72e+03 2.31e+00 bond pdb=" CA PHE B 925 " pdb=" C PHE B 925 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.30e-02 5.92e+03 2.16e+00 ... (remaining 24075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 32388 1.97 - 3.93: 274 3.93 - 5.90: 46 5.90 - 7.87: 7 7.87 - 9.84: 2 Bond angle restraints: 32717 Sorted by residual: angle pdb=" C ILE C 438 " pdb=" CA ILE C 438 " pdb=" CB ILE C 438 " ideal model delta sigma weight residual 111.65 107.21 4.44 1.22e+00 6.72e-01 1.33e+01 angle pdb=" N VAL C 927 " pdb=" CA VAL C 927 " pdb=" C VAL C 927 " ideal model delta sigma weight residual 111.58 107.88 3.70 1.06e+00 8.90e-01 1.22e+01 angle pdb=" N VAL B 927 " pdb=" CA VAL B 927 " pdb=" C VAL B 927 " ideal model delta sigma weight residual 112.98 108.90 4.08 1.25e+00 6.40e-01 1.07e+01 angle pdb=" C ASP C 637 " pdb=" N SER C 638 " pdb=" CA SER C 638 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N LEU B 929 " pdb=" CA LEU B 929 " pdb=" C LEU B 929 " ideal model delta sigma weight residual 111.82 108.28 3.54 1.16e+00 7.43e-01 9.29e+00 ... (remaining 32712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.90: 13385 13.90 - 27.79: 752 27.79 - 41.69: 186 41.69 - 55.58: 48 55.58 - 69.48: 10 Dihedral angle restraints: 14381 sinusoidal: 5495 harmonic: 8886 Sorted by residual: dihedral pdb=" CA GLN B 218 " pdb=" C GLN B 218 " pdb=" N LEU B 219 " pdb=" CA LEU B 219 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ILE C 943 " pdb=" C ILE C 943 " pdb=" N VAL C 944 " pdb=" CA VAL C 944 " ideal model delta harmonic sigma weight residual 180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA LEU B 534 " pdb=" C LEU B 534 " pdb=" N HIS B 535 " pdb=" CA HIS B 535 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 14378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2476 0.028 - 0.056: 865 0.056 - 0.084: 290 0.084 - 0.112: 162 0.112 - 0.140: 16 Chirality restraints: 3809 Sorted by residual: chirality pdb=" CA THR C 489 " pdb=" N THR C 489 " pdb=" C THR C 489 " pdb=" CB THR C 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 466 " pdb=" N ILE B 466 " pdb=" C ILE B 466 " pdb=" CB ILE B 466 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3806 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 427 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C THR B 250 " -0.022 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 872 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C PRO B 872 " 0.022 2.00e-02 2.50e+03 pdb=" O PRO B 872 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA B 873 " -0.007 2.00e-02 2.50e+03 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3203 2.75 - 3.29: 24034 3.29 - 3.83: 40676 3.83 - 4.36: 47148 4.36 - 4.90: 83461 Nonbonded interactions: 198522 Sorted by model distance: nonbonded pdb=" N ASP B 603 " pdb=" OD1 ASP B 603 " model vdw 2.213 3.120 nonbonded pdb=" OG SER A 561 " pdb=" OE1 GLU A 920 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 153 " pdb=" OH TYR A 182 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP B 311 " pdb=" OH TYR B 323 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 46 " pdb=" OG1 THR B 128 " model vdw 2.244 3.040 ... (remaining 198517 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 1 through 507 or (resid 508 through 509 and (name N or nam \ e CA or name C or name O or name CB )) or resid 510 through 1031)) selection = (chain 'B' and (resid 1 through 500 or (resid 501 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 1031)) selection = (chain 'C' and (resid 1 through 507 or (resid 508 through 509 and (name N or nam \ e CA or name C or name O or name CB )) or resid 510 through 1031)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.500 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 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 0.041 24080 Z= 0.167 Angle : 0.519 9.837 32717 Z= 0.297 Chirality : 0.037 0.140 3809 Planarity : 0.003 0.039 4219 Dihedral : 9.853 69.476 8677 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.91 % Allowed : 5.65 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.77 (0.16), residues: 3089 helix: 2.28 (0.13), residues: 1704 sheet: -0.48 (0.25), residues: 469 loop : 0.07 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 636 TYR 0.008 0.001 TYR C 327 PHE 0.012 0.001 PHE A1030 TRP 0.013 0.001 TRP A 540 HIS 0.002 0.000 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00320 (24080) covalent geometry : angle 0.51897 (32717) hydrogen bonds : bond 0.15381 ( 1550) hydrogen bonds : angle 6.67276 ( 4743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 791 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 804 THR cc_start: 0.7427 (m) cc_final: 0.7152 (m) outliers start: 73 outliers final: 12 residues processed: 847 average time/residue: 0.1508 time to fit residues: 196.2159 Evaluate side-chains 483 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 471 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 391 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 55 GLN A 87 GLN A 105 GLN A 213 GLN A 237 GLN A 245 GLN A 254 ASN A 469 GLN A 517 GLN A 583 GLN A 585 GLN A 700 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 848 GLN A 921 ASN A 926 GLN A 955 HIS A 967 GLN B 55 GLN B 109 ASN B 136 ASN B 163 GLN B 170 ASN B 231 ASN B 235 ASN B 298 ASN B 315 GLN B 592 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 ASN B 870 GLN B 926 GLN B 967 GLN C 55 GLN C 87 GLN C 123 GLN C 152 GLN C 218 GLN C 235 ASN C 241 GLN C 254 ASN C 308 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN C 655 ASN C 656 GLN C 684 GLN C 686 HIS C 691 HIS C 700 GLN C 735 GLN C 745 ASN C 749 GLN C 963 HIS C 967 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117882 restraints weight = 29664.719| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.07 r_work: 0.3270 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 24080 Z= 0.187 Angle : 0.649 11.390 32717 Z= 0.337 Chirality : 0.043 0.170 3809 Planarity : 0.004 0.059 4219 Dihedral : 4.586 55.054 3339 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.30 % Allowed : 13.61 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.42 (0.15), residues: 3089 helix: 1.86 (0.12), residues: 1724 sheet: -0.44 (0.24), residues: 455 loop : 0.04 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 536 TYR 0.019 0.002 TYR A 182 PHE 0.020 0.002 PHE A 571 TRP 0.026 0.002 TRP A 540 HIS 0.009 0.002 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00429 (24080) covalent geometry : angle 0.64867 (32717) hydrogen bonds : bond 0.04378 ( 1550) hydrogen bonds : angle 4.98047 ( 4743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 551 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.8131 (t) cc_final: 0.7869 (t) REVERT: A 357 LEU cc_start: 0.7006 (tp) cc_final: 0.6621 (mt) REVERT: A 498 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7491 (mtmm) REVERT: A 524 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6687 (mm-30) REVERT: A 535 HIS cc_start: 0.5009 (m170) cc_final: 0.4778 (m90) REVERT: A 841 ILE cc_start: 0.7868 (mm) cc_final: 0.7659 (mt) REVERT: A 916 MET cc_start: 0.7179 (mmm) cc_final: 0.6946 (tmm) REVERT: A 959 GLU cc_start: 0.7175 (tt0) cc_final: 0.6418 (mm-30) REVERT: B 170 ASN cc_start: 0.7603 (m110) cc_final: 0.7334 (m110) REVERT: B 437 GLN cc_start: 0.8368 (tt0) cc_final: 0.8145 (mt0) REVERT: B 521 ARG cc_start: 0.7882 (ptp-170) cc_final: 0.7488 (ptp-170) REVERT: B 596 TYR cc_start: 0.8795 (t80) cc_final: 0.8144 (t80) REVERT: B 950 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5569 (mtp) REVERT: B 1008 MET cc_start: 0.7754 (mmm) cc_final: 0.7496 (tpp) REVERT: C 274 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7625 (mmtt) REVERT: C 312 GLU cc_start: 0.8079 (tt0) cc_final: 0.7795 (tt0) REVERT: C 428 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.6977 (tpt-90) REVERT: C 524 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7435 (mm-30) REVERT: C 539 ARG cc_start: 0.7933 (tpt90) cc_final: 0.7282 (ttm-80) REVERT: C 661 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7701 (mtp85) REVERT: C 817 TYR cc_start: 0.8559 (t80) cc_final: 0.7965 (t80) REVERT: C 860 MET cc_start: 0.7769 (mmm) cc_final: 0.6980 (mmm) REVERT: C 897 PHE cc_start: 0.7741 (m-80) cc_final: 0.7396 (t80) outliers start: 83 outliers final: 45 residues processed: 608 average time/residue: 0.1337 time to fit residues: 131.4734 Evaluate side-chains 477 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 431 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 922 ASP Chi-restraints excluded: chain B residue 950 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 905 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 145 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 287 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 254 ASN A 361 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 926 GLN B 105 GLN B 315 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN C 170 ASN C 415 ASN C 437 GLN C 517 GLN C 863 GLN C 951 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113461 restraints weight = 29899.308| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.15 r_work: 0.3205 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24080 Z= 0.238 Angle : 0.674 16.842 32717 Z= 0.347 Chirality : 0.045 0.194 3809 Planarity : 0.005 0.056 4219 Dihedral : 4.524 45.711 3328 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.90 % Allowed : 15.13 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.10 (0.15), residues: 3089 helix: 1.58 (0.12), residues: 1731 sheet: -0.63 (0.25), residues: 438 loop : -0.04 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 8 TYR 0.028 0.002 TYR B 182 PHE 0.021 0.002 PHE C 4 TRP 0.015 0.002 TRP A 514 HIS 0.007 0.002 HIS B 686 Details of bonding type rmsd covalent geometry : bond 0.00558 (24080) covalent geometry : angle 0.67376 (32717) hydrogen bonds : bond 0.05062 ( 1550) hydrogen bonds : angle 5.01954 ( 4743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 526 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8757 (tp30) cc_final: 0.8474 (tp30) REVERT: A 182 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 254 ASN cc_start: 0.7320 (m-40) cc_final: 0.6995 (m110) REVERT: A 274 LYS cc_start: 0.7971 (mttt) cc_final: 0.7650 (mmmm) REVERT: A 355 MET cc_start: 0.8033 (mmt) cc_final: 0.7770 (mmt) REVERT: A 429 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6843 (tp30) REVERT: A 462 THR cc_start: 0.7677 (m) cc_final: 0.7448 (t) REVERT: A 498 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7779 (mtmm) REVERT: A 517 GLN cc_start: 0.7874 (tt0) cc_final: 0.7382 (tp40) REVERT: A 522 ASN cc_start: 0.8035 (m-40) cc_final: 0.7794 (m110) REVERT: A 535 HIS cc_start: 0.5798 (m170) cc_final: 0.5508 (m90) REVERT: A 749 GLN cc_start: 0.7809 (tt0) cc_final: 0.7556 (mt0) REVERT: A 839 MET cc_start: 0.6503 (mmm) cc_final: 0.5499 (ttm) REVERT: A 916 MET cc_start: 0.7349 (mmm) cc_final: 0.7062 (tmm) REVERT: A 942 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 959 GLU cc_start: 0.7686 (tt0) cc_final: 0.7078 (mm-30) REVERT: B 81 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: B 124 ASN cc_start: 0.8602 (t0) cc_final: 0.8381 (t0) REVERT: B 211 ASN cc_start: 0.7869 (t0) cc_final: 0.7539 (t0) REVERT: B 355 MET cc_start: 0.7005 (mmm) cc_final: 0.6717 (mtt) REVERT: B 359 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 422 GLU cc_start: 0.7408 (pt0) cc_final: 0.6734 (pt0) REVERT: B 425 LEU cc_start: 0.8029 (mt) cc_final: 0.7706 (mt) REVERT: B 478 MET cc_start: 0.8978 (mmp) cc_final: 0.8655 (mmm) REVERT: B 518 MET cc_start: 0.8340 (tmm) cc_final: 0.8011 (tmm) REVERT: B 521 ARG cc_start: 0.8187 (ptp-170) cc_final: 0.7982 (ptp90) REVERT: B 525 ARG cc_start: 0.8660 (ttm110) cc_final: 0.6907 (ttt-90) REVERT: B 595 LYS cc_start: 0.8785 (tttt) cc_final: 0.8337 (ttmt) REVERT: B 737 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8324 (mm) REVERT: B 842 MET cc_start: 0.8706 (tpt) cc_final: 0.8473 (mmp) REVERT: B 889 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8788 (tt) REVERT: B 976 SER cc_start: 0.9079 (t) cc_final: 0.8598 (m) REVERT: B 1013 ILE cc_start: 0.9044 (pt) cc_final: 0.8778 (tp) REVERT: C 20 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8363 (m) REVERT: C 130 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7906 (mmm160) REVERT: C 274 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8235 (mmpt) REVERT: C 323 TYR cc_start: 0.8994 (p90) cc_final: 0.7945 (p90) REVERT: C 328 GLU cc_start: 0.7857 (pt0) cc_final: 0.7570 (tt0) REVERT: C 514 TRP cc_start: 0.8097 (t60) cc_final: 0.7795 (t60) REVERT: C 539 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7608 (ttt-90) REVERT: C 547 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 659 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: C 746 ASP cc_start: 0.8039 (t0) cc_final: 0.7823 (t0) REVERT: C 839 MET cc_start: 0.6905 (mtt) cc_final: 0.6516 (mtt) REVERT: C 857 TRP cc_start: 0.7696 (m100) cc_final: 0.6972 (m100) REVERT: C 860 MET cc_start: 0.8492 (mmm) cc_final: 0.7643 (tpt) REVERT: C 900 MET cc_start: 0.8627 (mmm) cc_final: 0.8145 (mmm) REVERT: C 920 GLU cc_start: 0.7392 (tt0) cc_final: 0.7133 (tt0) REVERT: C 945 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: C 959 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: C 973 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7572 (mp) REVERT: C 986 MET cc_start: 0.8645 (ttt) cc_final: 0.8415 (ttp) outliers start: 123 outliers final: 62 residues processed: 615 average time/residue: 0.1501 time to fit residues: 147.7058 Evaluate side-chains 505 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 431 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 945 GLU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 227 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 717 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115976 restraints weight = 29424.287| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.93 r_work: 0.3193 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24080 Z= 0.144 Angle : 0.554 10.835 32717 Z= 0.284 Chirality : 0.040 0.166 3809 Planarity : 0.004 0.037 4219 Dihedral : 4.137 45.917 3324 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.86 % Allowed : 17.68 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.39 (0.15), residues: 3089 helix: 1.84 (0.12), residues: 1732 sheet: -0.53 (0.24), residues: 445 loop : 0.03 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.014 0.001 TYR A 875 PHE 0.013 0.001 PHE B1030 TRP 0.012 0.001 TRP C 787 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00336 (24080) covalent geometry : angle 0.55396 (32717) hydrogen bonds : bond 0.04015 ( 1550) hydrogen bonds : angle 4.66077 ( 4743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 441 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7457 (ttt90) REVERT: A 102 GLU cc_start: 0.8587 (tp30) cc_final: 0.8260 (tp30) REVERT: A 182 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: A 254 ASN cc_start: 0.7195 (m-40) cc_final: 0.6966 (m110) REVERT: A 274 LYS cc_start: 0.7793 (mttt) cc_final: 0.7395 (mmmm) REVERT: A 312 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 429 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6481 (tp30) REVERT: A 462 THR cc_start: 0.7606 (m) cc_final: 0.7393 (t) REVERT: A 498 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7611 (mtmm) REVERT: A 517 GLN cc_start: 0.7867 (tt0) cc_final: 0.7379 (tp40) REVERT: A 524 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 535 HIS cc_start: 0.5714 (m170) cc_final: 0.5385 (m90) REVERT: A 536 ARG cc_start: 0.7871 (tpt-90) cc_final: 0.7440 (mtp180) REVERT: A 749 GLN cc_start: 0.7783 (tt0) cc_final: 0.7430 (mt0) REVERT: A 806 ARG cc_start: 0.7813 (ptt-90) cc_final: 0.7527 (ptt90) REVERT: A 839 MET cc_start: 0.5517 (mmm) cc_final: 0.4990 (ttm) REVERT: A 916 MET cc_start: 0.7286 (mmm) cc_final: 0.6953 (tmm) REVERT: A 953 LYS cc_start: 0.7654 (tttt) cc_final: 0.7020 (pptt) REVERT: A 959 GLU cc_start: 0.7411 (tt0) cc_final: 0.6726 (mm-30) REVERT: B 32 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8596 (t) REVERT: B 81 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: B 112 GLN cc_start: 0.7854 (tp40) cc_final: 0.7587 (tp40) REVERT: B 115 MET cc_start: 0.7495 (tpp) cc_final: 0.7218 (mmm) REVERT: B 124 ASN cc_start: 0.8575 (t0) cc_final: 0.8319 (t0) REVERT: B 164 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 211 ASN cc_start: 0.7872 (t0) cc_final: 0.7359 (t0) REVERT: B 355 MET cc_start: 0.6890 (mmm) cc_final: 0.6378 (mtt) REVERT: B 359 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7499 (mt) REVERT: B 425 LEU cc_start: 0.8117 (mt) cc_final: 0.7704 (mt) REVERT: B 518 MET cc_start: 0.8240 (tmm) cc_final: 0.7844 (tmm) REVERT: B 525 ARG cc_start: 0.8465 (ttm110) cc_final: 0.6734 (ttp80) REVERT: B 595 LYS cc_start: 0.8462 (tttt) cc_final: 0.7913 (ttmt) REVERT: B 601 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 659 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 737 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8049 (mm) REVERT: B 842 MET cc_start: 0.8521 (tpt) cc_final: 0.8310 (mmm) REVERT: B 889 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 976 SER cc_start: 0.8873 (t) cc_final: 0.8480 (m) REVERT: B 1013 ILE cc_start: 0.8948 (pt) cc_final: 0.8588 (tp) REVERT: B 1029 ARG cc_start: 0.8050 (tpt90) cc_final: 0.7732 (tpt90) REVERT: C 130 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7731 (mmm160) REVERT: C 227 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8189 (ptpp) REVERT: C 274 LYS cc_start: 0.8593 (mtpt) cc_final: 0.7810 (mmtt) REVERT: C 323 TYR cc_start: 0.9009 (p90) cc_final: 0.7999 (p90) REVERT: C 539 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7289 (ttm-80) REVERT: C 547 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7323 (mp) REVERT: C 804 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7617 (p) REVERT: C 857 TRP cc_start: 0.7602 (m100) cc_final: 0.7079 (m100) REVERT: C 860 MET cc_start: 0.8186 (mmm) cc_final: 0.7161 (tpt) REVERT: C 897 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 900 MET cc_start: 0.8333 (mmm) cc_final: 0.7843 (mmm) REVERT: C 949 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7429 (mt-10) REVERT: C 959 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: C 973 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7174 (mp) outliers start: 97 outliers final: 50 residues processed: 512 average time/residue: 0.1500 time to fit residues: 122.8026 Evaluate side-chains 459 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 397 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 94 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 361 ASN A 516 ASN A 717 ASN B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113062 restraints weight = 29642.862| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.16 r_work: 0.3199 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24080 Z= 0.128 Angle : 0.532 9.137 32717 Z= 0.270 Chirality : 0.040 0.217 3809 Planarity : 0.003 0.041 4219 Dihedral : 4.025 47.529 3324 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.98 % Allowed : 17.56 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.53 (0.15), residues: 3089 helix: 1.97 (0.12), residues: 1732 sheet: -0.54 (0.24), residues: 441 loop : 0.08 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 418 TYR 0.014 0.001 TYR C 275 PHE 0.013 0.001 PHE B 571 TRP 0.011 0.001 TRP C 787 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00295 (24080) covalent geometry : angle 0.53244 (32717) hydrogen bonds : bond 0.03772 ( 1550) hydrogen bonds : angle 4.51056 ( 4743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 448 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8769 (tp30) cc_final: 0.8468 (tp30) REVERT: A 149 MET cc_start: 0.7781 (mtp) cc_final: 0.7562 (mtp) REVERT: A 182 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: A 254 ASN cc_start: 0.7408 (m-40) cc_final: 0.7188 (m110) REVERT: A 274 LYS cc_start: 0.7933 (mttt) cc_final: 0.7621 (mmmm) REVERT: A 312 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 338 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6785 (mt-10) REVERT: A 361 ASN cc_start: 0.7852 (t0) cc_final: 0.7635 (t0) REVERT: A 429 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6767 (tp30) REVERT: A 449 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 456 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8839 (ptp) REVERT: A 462 THR cc_start: 0.7856 (m) cc_final: 0.7646 (t) REVERT: A 498 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7642 (mtmm) REVERT: A 517 GLN cc_start: 0.7852 (tt0) cc_final: 0.7441 (tp40) REVERT: A 524 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 535 HIS cc_start: 0.5855 (m170) cc_final: 0.5364 (m170) REVERT: A 536 ARG cc_start: 0.7895 (tpt-90) cc_final: 0.7548 (mtp180) REVERT: A 538 LEU cc_start: 0.7688 (tp) cc_final: 0.6768 (mp) REVERT: A 656 GLN cc_start: 0.8422 (tt0) cc_final: 0.7932 (mm110) REVERT: A 749 GLN cc_start: 0.7965 (tt0) cc_final: 0.7664 (mt0) REVERT: A 799 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 806 ARG cc_start: 0.8163 (ptt-90) cc_final: 0.7876 (ptt90) REVERT: A 839 MET cc_start: 0.5758 (mmm) cc_final: 0.5268 (ttm) REVERT: A 916 MET cc_start: 0.7349 (mmm) cc_final: 0.7004 (tmm) REVERT: A 959 GLU cc_start: 0.7704 (tt0) cc_final: 0.7247 (mm-30) REVERT: B 32 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8864 (t) REVERT: B 117 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8210 (mtmt) REVERT: B 124 ASN cc_start: 0.8404 (t0) cc_final: 0.8101 (t0) REVERT: B 164 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: B 273 GLU cc_start: 0.8372 (tt0) cc_final: 0.8130 (tt0) REVERT: B 322 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7924 (mp0) REVERT: B 355 MET cc_start: 0.7050 (mmm) cc_final: 0.6693 (mtt) REVERT: B 359 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7667 (mt) REVERT: B 518 MET cc_start: 0.8352 (tmm) cc_final: 0.7945 (tmm) REVERT: B 525 ARG cc_start: 0.8696 (ttm110) cc_final: 0.7007 (ttp80) REVERT: B 595 LYS cc_start: 0.8768 (tttt) cc_final: 0.8207 (ttpt) REVERT: B 731 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7304 (mm-40) REVERT: B 737 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8332 (mm) REVERT: B 889 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 976 SER cc_start: 0.9061 (t) cc_final: 0.8798 (m) REVERT: B 1013 ILE cc_start: 0.8903 (pt) cc_final: 0.8565 (tp) REVERT: B 1029 ARG cc_start: 0.8318 (tpt90) cc_final: 0.7952 (tpt90) REVERT: C 87 GLN cc_start: 0.8081 (tt0) cc_final: 0.7512 (mm-40) REVERT: C 130 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7934 (mmt90) REVERT: C 227 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8309 (ptpp) REVERT: C 274 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8122 (mmtt) REVERT: C 323 TYR cc_start: 0.8977 (p90) cc_final: 0.8121 (p90) REVERT: C 524 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7697 (mm-30) REVERT: C 539 ARG cc_start: 0.8287 (tpt90) cc_final: 0.7925 (ttt-90) REVERT: C 547 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7662 (mp) REVERT: C 804 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7903 (p) REVERT: C 857 TRP cc_start: 0.7699 (m100) cc_final: 0.7285 (m100) REVERT: C 860 MET cc_start: 0.8475 (mmm) cc_final: 0.7363 (tpt) REVERT: C 897 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7808 (t80) REVERT: C 900 MET cc_start: 0.8564 (mmm) cc_final: 0.8148 (mmm) REVERT: C 920 GLU cc_start: 0.7408 (tt0) cc_final: 0.7004 (tt0) REVERT: C 973 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7665 (mp) outliers start: 100 outliers final: 61 residues processed: 519 average time/residue: 0.1560 time to fit residues: 128.6461 Evaluate side-chains 493 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 418 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 267 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 516 ASN A 708 ASN B 81 GLN B 237 GLN B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 520 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112861 restraints weight = 29683.293| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3199 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24080 Z= 0.146 Angle : 0.535 8.919 32717 Z= 0.273 Chirality : 0.040 0.171 3809 Planarity : 0.003 0.042 4219 Dihedral : 4.007 47.586 3324 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.06 % Allowed : 17.60 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.55 (0.15), residues: 3089 helix: 2.01 (0.12), residues: 1732 sheet: -0.54 (0.24), residues: 439 loop : 0.07 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 428 TYR 0.014 0.001 TYR A 875 PHE 0.012 0.001 PHE B 571 TRP 0.010 0.001 TRP C 787 HIS 0.014 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00345 (24080) covalent geometry : angle 0.53474 (32717) hydrogen bonds : bond 0.03837 ( 1550) hydrogen bonds : angle 4.49132 ( 4743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 431 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8766 (tp30) cc_final: 0.8404 (tp30) REVERT: A 108 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7462 (tp40) REVERT: A 182 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: A 225 VAL cc_start: 0.8370 (t) cc_final: 0.7966 (m) REVERT: A 248 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8320 (t70) REVERT: A 274 LYS cc_start: 0.8003 (mttt) cc_final: 0.7710 (mmmm) REVERT: A 312 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6854 (tm-30) REVERT: A 338 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6728 (mt-10) REVERT: A 429 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6775 (tp30) REVERT: A 472 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7861 (mt) REVERT: A 498 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7650 (mtmm) REVERT: A 517 GLN cc_start: 0.7905 (tt0) cc_final: 0.7465 (tp40) REVERT: A 535 HIS cc_start: 0.6033 (m170) cc_final: 0.5670 (m170) REVERT: A 536 ARG cc_start: 0.7805 (tpt-90) cc_final: 0.7310 (mtp180) REVERT: A 538 LEU cc_start: 0.7709 (tp) cc_final: 0.6802 (mp) REVERT: A 539 ARG cc_start: 0.7338 (ttt180) cc_final: 0.7033 (ptm160) REVERT: A 557 ARG cc_start: 0.6710 (tpp-160) cc_final: 0.6407 (tpp-160) REVERT: A 656 GLN cc_start: 0.8396 (tt0) cc_final: 0.7918 (mm110) REVERT: A 712 THR cc_start: 0.6163 (OUTLIER) cc_final: 0.5957 (p) REVERT: A 749 GLN cc_start: 0.8051 (tt0) cc_final: 0.7678 (mt0) REVERT: A 799 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 806 ARG cc_start: 0.8241 (ptt-90) cc_final: 0.7814 (ptt90) REVERT: A 916 MET cc_start: 0.7295 (mmm) cc_final: 0.6961 (tmm) REVERT: A 959 GLU cc_start: 0.7756 (tt0) cc_final: 0.7344 (mm-30) REVERT: A 986 MET cc_start: 0.7769 (ttm) cc_final: 0.7249 (ttm) REVERT: B 32 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8848 (t) REVERT: B 112 GLN cc_start: 0.7851 (tp40) cc_final: 0.7320 (mm-40) REVERT: B 124 ASN cc_start: 0.8357 (t0) cc_final: 0.8048 (t0) REVERT: B 164 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 194 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8370 (t0) REVERT: B 273 GLU cc_start: 0.8458 (tt0) cc_final: 0.8205 (tt0) REVERT: B 322 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7898 (mp0) REVERT: B 355 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6661 (mtt) REVERT: B 359 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7671 (mt) REVERT: B 518 MET cc_start: 0.8386 (tmm) cc_final: 0.7976 (tmm) REVERT: B 525 ARG cc_start: 0.8751 (ttm110) cc_final: 0.7023 (ttp80) REVERT: B 595 LYS cc_start: 0.8800 (tttt) cc_final: 0.8233 (ttpt) REVERT: B 635 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 731 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7262 (mm-40) REVERT: B 737 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 889 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8780 (tp) REVERT: B 900 MET cc_start: 0.8728 (tpp) cc_final: 0.8361 (mmm) REVERT: B 976 SER cc_start: 0.9153 (t) cc_final: 0.8912 (m) REVERT: B 1013 ILE cc_start: 0.8915 (pt) cc_final: 0.8595 (tp) REVERT: B 1029 ARG cc_start: 0.8385 (tpt90) cc_final: 0.7993 (tpt90) REVERT: C 66 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8231 (mm-30) REVERT: C 87 GLN cc_start: 0.8179 (tt0) cc_final: 0.7622 (mm-40) REVERT: C 227 LYS cc_start: 0.8634 (ptpp) cc_final: 0.8400 (ptpp) REVERT: C 274 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8147 (mmtt) REVERT: C 517 GLN cc_start: 0.7931 (pt0) cc_final: 0.7640 (pp30) REVERT: C 524 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7669 (mm-30) REVERT: C 539 ARG cc_start: 0.8104 (tpt90) cc_final: 0.7277 (ptm160) REVERT: C 547 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 601 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8045 (mt-10) REVERT: C 804 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 860 MET cc_start: 0.8535 (mmm) cc_final: 0.7270 (tpt) REVERT: C 897 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 900 MET cc_start: 0.8561 (mmm) cc_final: 0.8201 (mmm) REVERT: C 949 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7614 (mt-10) REVERT: C 973 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7794 (mp) outliers start: 102 outliers final: 65 residues processed: 509 average time/residue: 0.1475 time to fit residues: 119.7746 Evaluate side-chains 480 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 398 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 469 GLN A 717 ASN B 81 GLN B 231 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113274 restraints weight = 29564.194| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.16 r_work: 0.3207 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24080 Z= 0.130 Angle : 0.531 8.627 32717 Z= 0.269 Chirality : 0.039 0.175 3809 Planarity : 0.003 0.043 4219 Dihedral : 3.958 48.191 3324 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.98 % Allowed : 17.87 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.60 (0.15), residues: 3089 helix: 2.05 (0.12), residues: 1728 sheet: -0.51 (0.24), residues: 429 loop : 0.05 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 130 TYR 0.013 0.001 TYR C 275 PHE 0.012 0.001 PHE B 553 TRP 0.018 0.001 TRP C 857 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00302 (24080) covalent geometry : angle 0.53061 (32717) hydrogen bonds : bond 0.03698 ( 1550) hydrogen bonds : angle 4.42713 ( 4743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 434 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8669 (tp30) cc_final: 0.8259 (tp30) REVERT: A 108 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7479 (tp40) REVERT: A 182 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: A 225 VAL cc_start: 0.8401 (t) cc_final: 0.8058 (m) REVERT: A 254 ASN cc_start: 0.7576 (m-40) cc_final: 0.7041 (m110) REVERT: A 274 LYS cc_start: 0.8062 (mttt) cc_final: 0.7769 (mmmm) REVERT: A 308 ASN cc_start: 0.8002 (m-40) cc_final: 0.7721 (m110) REVERT: A 312 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 338 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 429 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6755 (tp30) REVERT: A 472 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7820 (mt) REVERT: A 498 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7704 (mtmm) REVERT: A 517 GLN cc_start: 0.7922 (tt0) cc_final: 0.7511 (tp40) REVERT: A 535 HIS cc_start: 0.6036 (m170) cc_final: 0.5631 (m170) REVERT: A 536 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7254 (mtp180) REVERT: A 538 LEU cc_start: 0.7796 (tp) cc_final: 0.6796 (mp) REVERT: A 539 ARG cc_start: 0.7340 (ttt180) cc_final: 0.7018 (ptm160) REVERT: A 551 MET cc_start: 0.7912 (ttp) cc_final: 0.7618 (ttp) REVERT: A 557 ARG cc_start: 0.6596 (tpp-160) cc_final: 0.6361 (tpp-160) REVERT: A 656 GLN cc_start: 0.8314 (tt0) cc_final: 0.7955 (mm110) REVERT: A 680 ASP cc_start: 0.7902 (t0) cc_final: 0.7560 (t0) REVERT: A 749 GLN cc_start: 0.8041 (tt0) cc_final: 0.7685 (mt0) REVERT: A 799 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 916 MET cc_start: 0.7240 (mmm) cc_final: 0.6979 (tmm) REVERT: A 950 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7594 (mtm) REVERT: A 953 LYS cc_start: 0.7573 (tttt) cc_final: 0.7077 (tmtt) REVERT: A 959 GLU cc_start: 0.7720 (tt0) cc_final: 0.7343 (mm-30) REVERT: A 986 MET cc_start: 0.7639 (ttm) cc_final: 0.7185 (ttm) REVERT: B 70 THR cc_start: 0.8540 (m) cc_final: 0.8324 (p) REVERT: B 112 GLN cc_start: 0.7885 (tp40) cc_final: 0.7363 (mm-40) REVERT: B 164 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 244 GLU cc_start: 0.8039 (tp30) cc_final: 0.7529 (mp0) REVERT: B 273 GLU cc_start: 0.8436 (tt0) cc_final: 0.8169 (tt0) REVERT: B 355 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6786 (mtt) REVERT: B 359 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7506 (mt) REVERT: B 419 ILE cc_start: 0.8495 (mm) cc_final: 0.8281 (mt) REVERT: B 521 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7581 (ptp-170) REVERT: B 525 ARG cc_start: 0.8753 (ttm110) cc_final: 0.7065 (ttp80) REVERT: B 595 LYS cc_start: 0.8756 (tttt) cc_final: 0.8221 (ttpt) REVERT: B 731 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7189 (mm-40) REVERT: B 737 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 889 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8812 (tp) REVERT: B 900 MET cc_start: 0.8726 (tpp) cc_final: 0.8357 (mmt) REVERT: B 976 SER cc_start: 0.9183 (t) cc_final: 0.8958 (m) REVERT: B 1013 ILE cc_start: 0.8895 (pt) cc_final: 0.8597 (tp) REVERT: B 1029 ARG cc_start: 0.8352 (tpt90) cc_final: 0.8116 (tpt90) REVERT: C 66 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7948 (mm-30) REVERT: C 87 GLN cc_start: 0.8223 (tt0) cc_final: 0.7673 (mm-40) REVERT: C 227 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8412 (ptpp) REVERT: C 274 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8123 (mmtt) REVERT: C 396 PHE cc_start: 0.9031 (m-10) cc_final: 0.8828 (m-10) REVERT: C 517 GLN cc_start: 0.8158 (pt0) cc_final: 0.7841 (pp30) REVERT: C 524 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7791 (mm-30) REVERT: C 539 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7391 (ttm-80) REVERT: C 547 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 804 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 839 MET cc_start: 0.7716 (mtm) cc_final: 0.7444 (mtt) REVERT: C 860 MET cc_start: 0.8403 (mmm) cc_final: 0.7349 (tpt) REVERT: C 897 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7699 (t80) REVERT: C 900 MET cc_start: 0.8606 (mmm) cc_final: 0.8290 (mmm) REVERT: C 949 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7626 (mt-10) REVERT: C 966 ARG cc_start: 0.7334 (mmt180) cc_final: 0.5962 (ttp-110) REVERT: C 973 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7694 (mp) outliers start: 100 outliers final: 65 residues processed: 508 average time/residue: 0.1379 time to fit residues: 113.5014 Evaluate side-chains 487 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 408 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 136 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 254 ASN B 315 GLN C 218 GLN C 391 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS C 955 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111531 restraints weight = 29587.397| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.15 r_work: 0.3183 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24080 Z= 0.152 Angle : 0.541 8.262 32717 Z= 0.276 Chirality : 0.040 0.205 3809 Planarity : 0.003 0.042 4219 Dihedral : 3.984 47.050 3324 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.14 % Allowed : 18.11 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.55 (0.15), residues: 3089 helix: 2.04 (0.12), residues: 1727 sheet: -0.55 (0.24), residues: 441 loop : 0.01 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 629 TYR 0.017 0.001 TYR A 316 PHE 0.014 0.001 PHE B 946 TRP 0.015 0.001 TRP A 857 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00366 (24080) covalent geometry : angle 0.54056 (32717) hydrogen bonds : bond 0.03802 ( 1550) hydrogen bonds : angle 4.45392 ( 4743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 409 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8706 (tp30) cc_final: 0.8231 (tp30) REVERT: A 108 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7394 (tp40) REVERT: A 182 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: A 225 VAL cc_start: 0.8563 (t) cc_final: 0.8216 (m) REVERT: A 248 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8350 (t70) REVERT: A 254 ASN cc_start: 0.7626 (m-40) cc_final: 0.6951 (m-40) REVERT: A 274 LYS cc_start: 0.8207 (mttt) cc_final: 0.7868 (mmmm) REVERT: A 312 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6672 (tm-30) REVERT: A 338 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 429 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6794 (tp30) REVERT: A 472 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 498 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7617 (mtmm) REVERT: A 517 GLN cc_start: 0.7980 (tt0) cc_final: 0.7541 (tp40) REVERT: A 535 HIS cc_start: 0.6276 (m170) cc_final: 0.5919 (m170) REVERT: A 536 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.7254 (mtp180) REVERT: A 538 LEU cc_start: 0.7729 (tp) cc_final: 0.6736 (mp) REVERT: A 539 ARG cc_start: 0.7306 (ttt180) cc_final: 0.6948 (ptm160) REVERT: A 551 MET cc_start: 0.7883 (ttp) cc_final: 0.7625 (ttp) REVERT: A 557 ARG cc_start: 0.6642 (tpp-160) cc_final: 0.6197 (tpp-160) REVERT: A 656 GLN cc_start: 0.8241 (tt0) cc_final: 0.7945 (mm110) REVERT: A 749 GLN cc_start: 0.8037 (tt0) cc_final: 0.7636 (mt0) REVERT: A 799 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7546 (t80) REVERT: A 953 LYS cc_start: 0.7559 (tttt) cc_final: 0.7075 (tmtt) REVERT: A 959 GLU cc_start: 0.7487 (tt0) cc_final: 0.7111 (mm-30) REVERT: A 986 MET cc_start: 0.7654 (ttm) cc_final: 0.7442 (ttp) REVERT: B 70 THR cc_start: 0.8668 (m) cc_final: 0.8387 (p) REVERT: B 112 GLN cc_start: 0.8031 (tp40) cc_final: 0.7481 (mm-40) REVERT: B 164 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: B 244 GLU cc_start: 0.8040 (tp30) cc_final: 0.7539 (mp0) REVERT: B 273 GLU cc_start: 0.8510 (tt0) cc_final: 0.8225 (tt0) REVERT: B 355 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6887 (mtt) REVERT: B 359 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7582 (mt) REVERT: B 419 ILE cc_start: 0.8508 (mm) cc_final: 0.8296 (mt) REVERT: B 525 ARG cc_start: 0.8826 (ttm110) cc_final: 0.7145 (ttp80) REVERT: B 570 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8667 (ptt) REVERT: B 595 LYS cc_start: 0.8724 (tttt) cc_final: 0.8161 (ttpt) REVERT: B 731 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7549 (mm-40) REVERT: B 737 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8349 (mm) REVERT: B 889 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (tp) REVERT: B 900 MET cc_start: 0.8708 (tpp) cc_final: 0.8398 (mmt) REVERT: B 976 SER cc_start: 0.9193 (t) cc_final: 0.8977 (m) REVERT: B 1013 ILE cc_start: 0.8894 (pt) cc_final: 0.8610 (tp) REVERT: B 1029 ARG cc_start: 0.8269 (tpt90) cc_final: 0.8031 (tpt90) REVERT: C 66 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7589 (mm-30) REVERT: C 87 GLN cc_start: 0.8286 (tt0) cc_final: 0.7685 (mm-40) REVERT: C 274 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8079 (mmtt) REVERT: C 338 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7130 (mt-10) REVERT: C 517 GLN cc_start: 0.8157 (pt0) cc_final: 0.7790 (pp30) REVERT: C 521 ARG cc_start: 0.7036 (ptm160) cc_final: 0.6433 (ptm-80) REVERT: C 539 ARG cc_start: 0.8095 (tpt90) cc_final: 0.7324 (ttm-80) REVERT: C 547 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8048 (mp) REVERT: C 842 MET cc_start: 0.7779 (tpp) cc_final: 0.7553 (tpp) REVERT: C 860 MET cc_start: 0.8136 (mmm) cc_final: 0.7000 (tpt) REVERT: C 897 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 900 MET cc_start: 0.8588 (mmm) cc_final: 0.8291 (mmm) REVERT: C 949 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7651 (mt-10) REVERT: C 966 ARG cc_start: 0.7429 (mmt180) cc_final: 0.6163 (ttp-110) REVERT: C 973 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7677 (mp) outliers start: 104 outliers final: 75 residues processed: 487 average time/residue: 0.1471 time to fit residues: 115.3946 Evaluate side-chains 481 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 392 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 291 optimal weight: 1.9990 chunk 125 optimal weight: 0.0050 chunk 250 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112733 restraints weight = 29738.099| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.16 r_work: 0.3181 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24080 Z= 0.127 Angle : 0.531 9.039 32717 Z= 0.270 Chirality : 0.039 0.220 3809 Planarity : 0.003 0.042 4219 Dihedral : 3.936 47.824 3324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.66 % Allowed : 18.87 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.62 (0.15), residues: 3089 helix: 2.08 (0.12), residues: 1729 sheet: -0.53 (0.24), residues: 443 loop : 0.07 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.024 0.001 TYR A 384 PHE 0.020 0.001 PHE B 946 TRP 0.028 0.001 TRP C 857 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00296 (24080) covalent geometry : angle 0.53112 (32717) hydrogen bonds : bond 0.03640 ( 1550) hydrogen bonds : angle 4.39129 ( 4743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 407 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7465 (p0) REVERT: A 102 GLU cc_start: 0.8647 (tp30) cc_final: 0.7849 (tp30) REVERT: A 108 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7374 (tp40) REVERT: A 182 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: A 202 ASP cc_start: 0.8114 (m-30) cc_final: 0.7832 (m-30) REVERT: A 225 VAL cc_start: 0.8539 (t) cc_final: 0.8197 (m) REVERT: A 248 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8256 (t70) REVERT: A 254 ASN cc_start: 0.7641 (m-40) cc_final: 0.6984 (m-40) REVERT: A 274 LYS cc_start: 0.8188 (mttt) cc_final: 0.7878 (mmmm) REVERT: A 308 ASN cc_start: 0.7892 (m-40) cc_final: 0.7617 (m110) REVERT: A 338 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 429 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6777 (tp30) REVERT: A 438 ILE cc_start: 0.8124 (tt) cc_final: 0.7713 (tt) REVERT: A 472 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7774 (mt) REVERT: A 498 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7450 (mtmm) REVERT: A 535 HIS cc_start: 0.6029 (m170) cc_final: 0.5714 (m170) REVERT: A 536 ARG cc_start: 0.7633 (tpt-90) cc_final: 0.7233 (mtp180) REVERT: A 538 LEU cc_start: 0.7809 (tp) cc_final: 0.6837 (mp) REVERT: A 539 ARG cc_start: 0.7280 (ttt180) cc_final: 0.6871 (ptm160) REVERT: A 551 MET cc_start: 0.7886 (ttp) cc_final: 0.7636 (ttt) REVERT: A 557 ARG cc_start: 0.6712 (tpp-160) cc_final: 0.6249 (tpp-160) REVERT: A 656 GLN cc_start: 0.8180 (tt0) cc_final: 0.7919 (mm110) REVERT: A 749 GLN cc_start: 0.8041 (tt0) cc_final: 0.7658 (mt0) REVERT: A 799 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 806 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.7777 (ptt-90) REVERT: A 916 MET cc_start: 0.7481 (tmm) cc_final: 0.7137 (mmm) REVERT: A 950 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7792 (mtm) REVERT: A 953 LYS cc_start: 0.7577 (tttt) cc_final: 0.7113 (tmtt) REVERT: A 959 GLU cc_start: 0.7457 (tt0) cc_final: 0.7135 (mm-30) REVERT: A 986 MET cc_start: 0.7599 (ttm) cc_final: 0.7195 (ttm) REVERT: B 70 THR cc_start: 0.8533 (m) cc_final: 0.8288 (p) REVERT: B 112 GLN cc_start: 0.7958 (tp40) cc_final: 0.7441 (mm-40) REVERT: B 164 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 244 GLU cc_start: 0.8132 (tp30) cc_final: 0.7539 (mp0) REVERT: B 273 GLU cc_start: 0.8456 (tt0) cc_final: 0.8210 (tt0) REVERT: B 419 ILE cc_start: 0.8499 (mm) cc_final: 0.8297 (mt) REVERT: B 521 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7537 (ptp-170) REVERT: B 525 ARG cc_start: 0.8846 (ttm110) cc_final: 0.7156 (ttp80) REVERT: B 570 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8609 (ptt) REVERT: B 595 LYS cc_start: 0.8657 (tttt) cc_final: 0.8124 (ttpt) REVERT: B 731 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: B 737 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 889 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8853 (tp) REVERT: B 900 MET cc_start: 0.8653 (tpp) cc_final: 0.8367 (mmt) REVERT: B 976 SER cc_start: 0.9182 (t) cc_final: 0.8973 (m) REVERT: B 1013 ILE cc_start: 0.8879 (pt) cc_final: 0.8605 (tp) REVERT: B 1029 ARG cc_start: 0.8282 (tpt90) cc_final: 0.8034 (tpt90) REVERT: C 66 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7564 (mm-30) REVERT: C 87 GLN cc_start: 0.8269 (tt0) cc_final: 0.7650 (mm-40) REVERT: C 274 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8034 (mmtt) REVERT: C 304 GLU cc_start: 0.8198 (pt0) cc_final: 0.7951 (tp30) REVERT: C 338 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7149 (mt-10) REVERT: C 517 GLN cc_start: 0.8182 (pt0) cc_final: 0.7819 (pp30) REVERT: C 521 ARG cc_start: 0.7154 (ptm160) cc_final: 0.6525 (ptm-80) REVERT: C 539 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7403 (ttm-80) REVERT: C 547 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8099 (mp) REVERT: C 860 MET cc_start: 0.8050 (mmm) cc_final: 0.6991 (tpt) REVERT: C 897 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 900 MET cc_start: 0.8578 (mmm) cc_final: 0.8291 (mmm) REVERT: C 946 PHE cc_start: 0.7933 (t80) cc_final: 0.7557 (t80) REVERT: C 949 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7659 (mt-10) REVERT: C 966 ARG cc_start: 0.7299 (mmt180) cc_final: 0.6251 (ttp-110) REVERT: C 973 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7736 (mp) outliers start: 92 outliers final: 68 residues processed: 473 average time/residue: 0.1514 time to fit residues: 115.2579 Evaluate side-chains 470 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 388 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 180 optimal weight: 0.3980 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 283 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 516 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112106 restraints weight = 29744.396| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.16 r_work: 0.3171 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.8203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24080 Z= 0.124 Angle : 0.530 9.683 32717 Z= 0.269 Chirality : 0.039 0.226 3809 Planarity : 0.003 0.043 4219 Dihedral : 3.901 48.628 3324 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.42 % Allowed : 19.07 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.65 (0.15), residues: 3089 helix: 2.10 (0.12), residues: 1730 sheet: -0.45 (0.24), residues: 438 loop : 0.06 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.023 0.001 TYR A 384 PHE 0.018 0.001 PHE B 946 TRP 0.023 0.001 TRP C 857 HIS 0.003 0.001 HIS B 686 Details of bonding type rmsd covalent geometry : bond 0.00289 (24080) covalent geometry : angle 0.53039 (32717) hydrogen bonds : bond 0.03561 ( 1550) hydrogen bonds : angle 4.35960 ( 4743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 415 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7414 (p0) REVERT: A 102 GLU cc_start: 0.8621 (tp30) cc_final: 0.7776 (tp30) REVERT: A 108 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7890 (tp40) REVERT: A 182 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 202 ASP cc_start: 0.8122 (m-30) cc_final: 0.7735 (m-30) REVERT: A 225 VAL cc_start: 0.8519 (t) cc_final: 0.8179 (m) REVERT: A 238 SER cc_start: 0.7483 (m) cc_final: 0.7181 (p) REVERT: A 248 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8267 (t70) REVERT: A 254 ASN cc_start: 0.7673 (m-40) cc_final: 0.7014 (m-40) REVERT: A 274 LYS cc_start: 0.8251 (mttt) cc_final: 0.7950 (mmtt) REVERT: A 308 ASN cc_start: 0.7900 (m-40) cc_final: 0.7635 (m110) REVERT: A 312 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 338 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 429 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6745 (tp30) REVERT: A 438 ILE cc_start: 0.8084 (tt) cc_final: 0.7662 (tt) REVERT: A 472 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 498 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7410 (mtmm) REVERT: A 535 HIS cc_start: 0.6192 (m170) cc_final: 0.5881 (m170) REVERT: A 536 ARG cc_start: 0.7620 (tpt-90) cc_final: 0.6984 (mmm-85) REVERT: A 538 LEU cc_start: 0.7800 (tp) cc_final: 0.6864 (mp) REVERT: A 539 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6867 (ptm160) REVERT: A 551 MET cc_start: 0.7881 (ttp) cc_final: 0.7663 (ttt) REVERT: A 557 ARG cc_start: 0.6853 (tpp-160) cc_final: 0.6427 (tpp-160) REVERT: A 749 GLN cc_start: 0.8055 (tt0) cc_final: 0.7667 (mt0) REVERT: A 799 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 806 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7857 (ptt-90) REVERT: A 916 MET cc_start: 0.7580 (tmm) cc_final: 0.7181 (mmm) REVERT: A 950 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: A 953 LYS cc_start: 0.7609 (tttt) cc_final: 0.7136 (tmtt) REVERT: A 959 GLU cc_start: 0.7391 (tt0) cc_final: 0.7129 (mm-30) REVERT: B 70 THR cc_start: 0.8483 (m) cc_final: 0.8239 (p) REVERT: B 164 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: B 182 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8304 (m-10) REVERT: B 244 GLU cc_start: 0.7966 (tp30) cc_final: 0.7414 (mp0) REVERT: B 273 GLU cc_start: 0.8474 (tt0) cc_final: 0.8213 (tt0) REVERT: B 521 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.7483 (ptp-170) REVERT: B 525 ARG cc_start: 0.8852 (ttm110) cc_final: 0.7163 (ttp80) REVERT: B 570 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (ptt) REVERT: B 595 LYS cc_start: 0.8648 (tttt) cc_final: 0.8109 (ttpt) REVERT: B 731 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7544 (mm-40) REVERT: B 737 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 889 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 900 MET cc_start: 0.8634 (tpp) cc_final: 0.8375 (mmt) REVERT: B 1013 ILE cc_start: 0.8855 (pt) cc_final: 0.8583 (tp) REVERT: B 1029 ARG cc_start: 0.8259 (tpt90) cc_final: 0.8016 (tpt90) REVERT: C 66 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7520 (mm-30) REVERT: C 68 ASN cc_start: 0.8339 (m-40) cc_final: 0.8116 (m110) REVERT: C 87 GLN cc_start: 0.8283 (tt0) cc_final: 0.7640 (mm-40) REVERT: C 274 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8375 (mmtt) REVERT: C 338 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7096 (mt-10) REVERT: C 517 GLN cc_start: 0.8137 (pt0) cc_final: 0.7819 (pp30) REVERT: C 536 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7847 (ttp80) REVERT: C 539 ARG cc_start: 0.8182 (tpt90) cc_final: 0.7369 (ptm160) REVERT: C 547 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8108 (mp) REVERT: C 796 MET cc_start: 0.8732 (mmm) cc_final: 0.8323 (mmm) REVERT: C 860 MET cc_start: 0.8110 (mmm) cc_final: 0.6985 (tpt) REVERT: C 897 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 900 MET cc_start: 0.8564 (mmm) cc_final: 0.8289 (mmm) REVERT: C 949 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7604 (mt-10) REVERT: C 966 ARG cc_start: 0.7449 (mmt180) cc_final: 0.6327 (ttp-110) REVERT: C 967 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7419 (tp-100) REVERT: C 973 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7739 (mp) outliers start: 86 outliers final: 65 residues processed: 476 average time/residue: 0.1497 time to fit residues: 113.7038 Evaluate side-chains 475 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 516 ASN Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 192 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 112 GLN A 656 GLN B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 415 ASN C 516 ASN ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 955 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113545 restraints weight = 29576.963| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.15 r_work: 0.3204 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24080 Z= 0.130 Angle : 0.536 9.733 32717 Z= 0.271 Chirality : 0.040 0.226 3809 Planarity : 0.003 0.044 4219 Dihedral : 3.899 48.657 3324 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.54 % Allowed : 19.47 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.65 (0.15), residues: 3089 helix: 2.09 (0.12), residues: 1731 sheet: -0.48 (0.24), residues: 441 loop : 0.08 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.024 0.001 TYR A 384 PHE 0.021 0.001 PHE B 946 TRP 0.021 0.001 TRP C 857 HIS 0.002 0.001 HIS C 955 Details of bonding type rmsd covalent geometry : bond 0.00306 (24080) covalent geometry : angle 0.53605 (32717) hydrogen bonds : bond 0.03581 ( 1550) hydrogen bonds : angle 4.36701 ( 4743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.96 seconds wall clock time: 103 minutes 16.68 seconds (6196.68 seconds total)