Starting phenix.real_space_refine on Fri Jun 20 04:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f3e_28848/06_2025/8f3e_28848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f3e_28848/06_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_28848/06_2025/8f3e_28848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f3e_28848/06_2025/8f3e_28848.map" model { file = "/net/cci-nas-00/data/ceres_data/8f3e_28848/06_2025/8f3e_28848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f3e_28848/06_2025/8f3e_28848.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2} 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: 14.60, per 1000 atoms: 0.62 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: 6.52 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.92 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: 10.70 Time building geometry restraints manager: 7.52 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: 2.920 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: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.650 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (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 TRP 0.013 0.001 TRP A 540 HIS 0.002 0.000 HIS A 691 PHE 0.012 0.001 PHE A1030 TYR 0.008 0.001 TYR C 327 ARG 0.002 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.15381 ( 1550) hydrogen bonds : angle 6.67276 ( 4743) covalent geometry : bond 0.00320 (24080) covalent geometry : angle 0.51897 (32717) *********************** 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 : 2.878 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: 0.3699 time to fit residues: 478.1720 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 : 2.696 ------------------------------------------------------------------------------- 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 260 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 242 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 952 GLN A 955 HIS B 55 GLN B 109 ASN B 112 GLN 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 170 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 700 GLN C 735 GLN C 745 ASN C 749 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118596 restraints weight = 29439.727| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.08 r_work: 0.3276 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24080 Z= 0.163 Angle : 0.603 10.570 32717 Z= 0.312 Chirality : 0.041 0.163 3809 Planarity : 0.004 0.052 4219 Dihedral : 4.440 56.228 3339 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.99 % Allowed : 13.61 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3089 helix: 2.04 (0.12), residues: 1727 sheet: -0.40 (0.24), residues: 469 loop : 0.03 (0.22), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 540 HIS 0.009 0.001 HIS C 963 PHE 0.018 0.002 PHE C 511 TYR 0.017 0.002 TYR A 862 ARG 0.008 0.001 ARG C 536 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 1550) hydrogen bonds : angle 5.00438 ( 4743) covalent geometry : bond 0.00377 (24080) covalent geometry : angle 0.60282 (32717) *********************** 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 597 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 522 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.8077 (t) cc_final: 0.7803 (t) REVERT: A 142 PHE cc_start: 0.6679 (m-80) cc_final: 0.6304 (m-80) REVERT: A 312 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 357 LEU cc_start: 0.6820 (tp) cc_final: 0.6536 (mt) REVERT: A 498 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7473 (mtmm) REVERT: A 524 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6547 (mm-30) REVERT: A 839 MET cc_start: 0.6904 (mmt) cc_final: 0.6536 (mmt) REVERT: A 950 MET cc_start: 0.7634 (mtt) cc_final: 0.7399 (mtt) REVERT: A 959 GLU cc_start: 0.7003 (tt0) cc_final: 0.6163 (mm-30) REVERT: B 138 LEU cc_start: 0.8581 (mt) cc_final: 0.8341 (mt) REVERT: B 226 ASP cc_start: 0.8379 (p0) cc_final: 0.7993 (m-30) REVERT: B 521 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7440 (ptp-170) REVERT: B 525 ARG cc_start: 0.7773 (ttm110) cc_final: 0.6449 (ttt-90) REVERT: B 596 TYR cc_start: 0.8625 (t80) cc_final: 0.8107 (t80) REVERT: B 724 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 950 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.5088 (mtp) REVERT: B 986 MET cc_start: 0.8061 (tpp) cc_final: 0.7646 (ttm) REVERT: C 6 ILE cc_start: 0.7625 (mt) cc_final: 0.7382 (mt) REVERT: C 428 ARG cc_start: 0.7319 (ttt-90) cc_final: 0.7005 (tpt90) REVERT: C 524 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7511 (mm-30) REVERT: C 539 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7288 (ttm-80) REVERT: C 817 TYR cc_start: 0.8489 (t80) cc_final: 0.8142 (t80) REVERT: C 860 MET cc_start: 0.7596 (mmm) cc_final: 0.6801 (tmm) REVERT: C 897 PHE cc_start: 0.7474 (m-80) cc_final: 0.7183 (t80) outliers start: 75 outliers final: 39 residues processed: 572 average time/residue: 0.3096 time to fit residues: 287.8166 Evaluate side-chains 478 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 437 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET 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 558 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 91 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 311 ASP 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 541 ILE 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 724 GLN 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 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 530 VAL Chi-restraints excluded: chain C residue 533 ILE 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 281 optimal weight: 0.0270 chunk 161 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 724 GLN A 926 GLN A 967 GLN B 112 GLN B 315 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 726 GLN B 921 ASN C 170 ASN C 308 ASN C 415 ASN C 437 GLN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 HIS C 967 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121011 restraints weight = 29180.871| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.69 r_work: 0.3283 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24080 Z= 0.199 Angle : 0.646 15.880 32717 Z= 0.335 Chirality : 0.045 0.276 3809 Planarity : 0.004 0.049 4219 Dihedral : 4.520 56.211 3330 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.34 % Allowed : 15.57 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3089 helix: 1.73 (0.12), residues: 1727 sheet: -0.40 (0.25), residues: 429 loop : 0.02 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 752 HIS 0.008 0.002 HIS C 955 PHE 0.029 0.002 PHE A 553 TYR 0.032 0.002 TYR B 182 ARG 0.010 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1550) hydrogen bonds : angle 4.87046 ( 4743) covalent geometry : bond 0.00447 (24080) covalent geometry : angle 0.64601 (32717) *********************** 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 670 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 561 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: A 254 ASN cc_start: 0.7084 (m-40) cc_final: 0.6861 (m110) REVERT: A 312 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 377 MET cc_start: 0.7779 (mmt) cc_final: 0.7524 (mmm) REVERT: A 498 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7601 (mtmm) REVERT: A 524 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 536 ARG cc_start: 0.8104 (tpt-90) cc_final: 0.7624 (mtp180) REVERT: A 839 MET cc_start: 0.7192 (mmt) cc_final: 0.6613 (mmt) REVERT: A 915 TRP cc_start: 0.7718 (t60) cc_final: 0.7506 (t-100) REVERT: A 959 GLU cc_start: 0.7632 (tt0) cc_final: 0.6994 (mm-30) REVERT: B 124 ASN cc_start: 0.8422 (t0) cc_final: 0.8209 (t0) REVERT: B 355 MET cc_start: 0.7122 (mmm) cc_final: 0.6641 (mtt) REVERT: B 359 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 398 MET cc_start: 0.8520 (mtt) cc_final: 0.8276 (mtt) REVERT: B 521 ARG cc_start: 0.8179 (ptp-170) cc_final: 0.7970 (ptp90) REVERT: B 525 ARG cc_start: 0.8506 (ttm110) cc_final: 0.6843 (ttt-90) REVERT: B 595 LYS cc_start: 0.8764 (tttt) cc_final: 0.8435 (ttmt) REVERT: B 659 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 737 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 986 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8700 (ttt) REVERT: B 1029 ARG cc_start: 0.8128 (tpm-80) cc_final: 0.7659 (tpt90) REVERT: C 274 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8322 (mmtt) REVERT: C 323 TYR cc_start: 0.8628 (p90) cc_final: 0.7891 (p90) REVERT: C 539 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7752 (ttt-90) REVERT: C 547 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7662 (mp) REVERT: C 659 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: C 804 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8035 (p) REVERT: C 842 MET cc_start: 0.7706 (mmt) cc_final: 0.7444 (tpp) REVERT: C 920 GLU cc_start: 0.7216 (tt0) cc_final: 0.6983 (tt0) REVERT: C 953 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7402 (mmmt) REVERT: C 959 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: C 963 HIS cc_start: 0.7760 (t-170) cc_final: 0.7541 (t70) outliers start: 109 outliers final: 54 residues processed: 634 average time/residue: 0.3732 time to fit residues: 373.8514 Evaluate side-chains 493 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR 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 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 604 ASN 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 955 HIS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 256 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 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 581 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 804 THR 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 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 986 MET Chi-restraints excluded: chain C residue 57 LEU 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 383 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 959 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 272 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 235 ASN A 708 ASN A 717 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 194 ASN B 211 ASN B 231 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN C 170 ASN C 235 ASN C 315 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 592 GLN C 951 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117887 restraints weight = 29450.506| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.93 r_work: 0.3241 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24080 Z= 0.137 Angle : 0.555 11.372 32717 Z= 0.282 Chirality : 0.040 0.171 3809 Planarity : 0.004 0.047 4219 Dihedral : 4.077 48.131 3325 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.98 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.15), residues: 3089 helix: 1.95 (0.12), residues: 1732 sheet: -0.43 (0.24), residues: 460 loop : 0.07 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 787 HIS 0.005 0.001 HIS C 955 PHE 0.014 0.001 PHE A 571 TYR 0.022 0.001 TYR A 384 ARG 0.010 0.001 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 1550) hydrogen bonds : angle 4.58041 ( 4743) covalent geometry : bond 0.00316 (24080) covalent geometry : angle 0.55466 (32717) *********************** 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 563 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 463 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7352 (ttt90) REVERT: A 87 GLN cc_start: 0.8634 (tt0) cc_final: 0.8433 (tt0) REVERT: A 102 GLU cc_start: 0.8574 (tp30) cc_final: 0.8246 (tp30) REVERT: A 108 GLN cc_start: 0.7937 (tp40) cc_final: 0.7648 (tp-100) REVERT: A 149 MET cc_start: 0.7446 (mtp) cc_final: 0.7156 (mtp) REVERT: A 182 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: A 254 ASN cc_start: 0.7049 (m-40) cc_final: 0.6782 (m110) REVERT: A 312 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 377 MET cc_start: 0.7531 (mmt) cc_final: 0.7308 (mmm) REVERT: A 462 THR cc_start: 0.7495 (m) cc_final: 0.7253 (t) REVERT: A 498 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7357 (mtmm) REVERT: A 524 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7046 (mm-30) REVERT: A 535 HIS cc_start: 0.6376 (m-70) cc_final: 0.6125 (m170) REVERT: A 536 ARG cc_start: 0.7789 (tpt-90) cc_final: 0.7084 (mmm-85) REVERT: A 626 MET cc_start: 0.7457 (mtm) cc_final: 0.7006 (mtt) REVERT: A 839 MET cc_start: 0.6902 (mmt) cc_final: 0.6480 (mmt) REVERT: A 953 LYS cc_start: 0.7708 (pttt) cc_final: 0.7431 (pptt) REVERT: A 959 GLU cc_start: 0.7505 (tt0) cc_final: 0.6719 (mm-30) REVERT: A 974 MET cc_start: 0.8700 (ttm) cc_final: 0.8453 (ttm) REVERT: B 116 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8159 (mmm160) REVERT: B 124 ASN cc_start: 0.8463 (t0) cc_final: 0.8233 (t0) REVERT: B 164 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: B 274 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8288 (mtmt) REVERT: B 305 LEU cc_start: 0.8036 (tp) cc_final: 0.7827 (mp) REVERT: B 355 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6318 (mtt) REVERT: B 359 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7585 (mt) REVERT: B 518 MET cc_start: 0.8052 (tmm) cc_final: 0.7697 (tmm) REVERT: B 525 ARG cc_start: 0.8491 (ttm110) cc_final: 0.6711 (ttt-90) REVERT: B 595 LYS cc_start: 0.8517 (tttt) cc_final: 0.8005 (ttmt) REVERT: B 659 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 737 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 842 MET cc_start: 0.8429 (tpt) cc_final: 0.8185 (mmp) REVERT: B 860 MET cc_start: 0.7874 (ttp) cc_final: 0.7607 (tpp) REVERT: B 889 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (tp) REVERT: B 976 SER cc_start: 0.8935 (t) cc_final: 0.8516 (m) REVERT: B 1029 ARG cc_start: 0.8137 (tpm-80) cc_final: 0.7796 (tpt90) REVERT: C 20 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7820 (m) REVERT: C 66 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7522 (mt-10) REVERT: C 95 LYS cc_start: 0.7936 (mttt) cc_final: 0.7715 (mttm) REVERT: C 134 ASP cc_start: 0.8160 (m-30) cc_final: 0.7520 (m-30) REVERT: C 227 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8239 (ptpp) REVERT: C 264 ASP cc_start: 0.8550 (t0) cc_final: 0.8316 (m-30) REVERT: C 274 LYS cc_start: 0.8601 (mtpt) cc_final: 0.7863 (mmtt) REVERT: C 323 TYR cc_start: 0.8805 (p90) cc_final: 0.7872 (p90) REVERT: C 524 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 539 ARG cc_start: 0.7848 (tpt90) cc_final: 0.7597 (ttt-90) REVERT: C 547 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7314 (mp) REVERT: C 824 GLU cc_start: 0.8427 (tt0) cc_final: 0.8177 (tt0) REVERT: C 860 MET cc_start: 0.8244 (mmm) cc_final: 0.7489 (tpt) REVERT: C 897 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 920 GLU cc_start: 0.7014 (tt0) cc_final: 0.6579 (tt0) REVERT: C 949 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 953 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7157 (mmmt) REVERT: C 959 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: C 963 HIS cc_start: 0.7349 (t-170) cc_final: 0.6924 (t70) outliers start: 100 outliers final: 51 residues processed: 535 average time/residue: 0.3427 time to fit residues: 290.8117 Evaluate side-chains 485 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 424 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 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 717 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 135 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 302 THR Chi-restraints excluded: chain B residue 306 VAL 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 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 737 LEU Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR 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 889 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 592 GLN 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 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 959 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 77 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 517 GLN A 724 GLN B 81 GLN B 211 ASN B 231 ASN B 308 ASN B 315 GLN B 621 GLN B 691 HIS ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN C 235 ASN C 315 GLN C 517 GLN C 600 HIS ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113919 restraints weight = 29714.678| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.17 r_work: 0.3204 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24080 Z= 0.154 Angle : 0.555 11.900 32717 Z= 0.283 Chirality : 0.040 0.163 3809 Planarity : 0.004 0.046 4219 Dihedral : 4.054 46.630 3325 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.90 % Allowed : 18.11 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3089 helix: 1.99 (0.12), residues: 1731 sheet: -0.43 (0.24), residues: 441 loop : 0.05 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 540 HIS 0.008 0.001 HIS A 716 PHE 0.016 0.001 PHE B 760 TYR 0.014 0.001 TYR B 597 ARG 0.008 0.001 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1550) hydrogen bonds : angle 4.53508 ( 4743) covalent geometry : bond 0.00364 (24080) covalent geometry : angle 0.55524 (32717) *********************** 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 540 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 442 time to evaluate : 2.455 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7867 (ttm110) REVERT: A 102 GLU cc_start: 0.8667 (tp30) cc_final: 0.8304 (tp30) REVERT: A 182 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: A 254 ASN cc_start: 0.7252 (m-40) cc_final: 0.6984 (m110) REVERT: A 312 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 338 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 429 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6773 (tp30) REVERT: A 462 THR cc_start: 0.7913 (m) cc_final: 0.7669 (t) REVERT: A 498 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7504 (mtmm) REVERT: A 536 ARG cc_start: 0.7759 (tpt-90) cc_final: 0.7160 (mmm-85) REVERT: A 557 ARG cc_start: 0.6961 (tpp-160) cc_final: 0.6742 (tpp-160) REVERT: A 581 SER cc_start: 0.7776 (m) cc_final: 0.7540 (p) REVERT: A 626 MET cc_start: 0.7776 (mtm) cc_final: 0.7449 (mtt) REVERT: A 749 GLN cc_start: 0.7908 (tt0) cc_final: 0.7563 (mt0) REVERT: A 806 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7888 (ptt90) REVERT: A 839 MET cc_start: 0.7119 (mmt) cc_final: 0.6642 (mmt) REVERT: A 953 LYS cc_start: 0.7696 (pttt) cc_final: 0.6832 (mtmm) REVERT: A 959 GLU cc_start: 0.7705 (tt0) cc_final: 0.7100 (mm-30) REVERT: A 966 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7561 (tpt-90) REVERT: B 124 ASN cc_start: 0.8527 (t0) cc_final: 0.8302 (t0) REVERT: B 164 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: B 355 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6734 (mtt) REVERT: B 359 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7734 (mt) REVERT: B 518 MET cc_start: 0.8151 (tmm) cc_final: 0.7741 (tmm) REVERT: B 521 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7758 (ptp-110) REVERT: B 525 ARG cc_start: 0.8653 (ttm110) cc_final: 0.6969 (ttp80) REVERT: B 595 LYS cc_start: 0.8748 (tttt) cc_final: 0.8214 (ttpt) REVERT: B 659 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 737 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 842 MET cc_start: 0.8681 (tpt) cc_final: 0.8436 (mmp) REVERT: B 889 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8565 (tp) REVERT: B 976 SER cc_start: 0.9207 (t) cc_final: 0.8839 (m) REVERT: B 1029 ARG cc_start: 0.8211 (tpm-80) cc_final: 0.7829 (tpt90) REVERT: C 20 CYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8292 (m) REVERT: C 130 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7804 (mmt90) REVERT: C 134 ASP cc_start: 0.8177 (m-30) cc_final: 0.7658 (m-30) REVERT: C 227 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8294 (ptpp) REVERT: C 274 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8156 (mmtt) REVERT: C 323 TYR cc_start: 0.9032 (p90) cc_final: 0.8224 (p90) REVERT: C 383 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 539 ARG cc_start: 0.8224 (tpt90) cc_final: 0.7912 (tpt90) REVERT: C 547 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7758 (mp) REVERT: C 897 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7842 (t80) REVERT: C 900 MET cc_start: 0.8601 (mmm) cc_final: 0.8214 (mmm) REVERT: C 920 GLU cc_start: 0.7297 (tt0) cc_final: 0.6945 (tt0) REVERT: C 953 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7277 (mmmt) REVERT: C 963 HIS cc_start: 0.7705 (t-170) cc_final: 0.7344 (t-90) outliers start: 98 outliers final: 58 residues processed: 517 average time/residue: 0.3356 time to fit residues: 274.8000 Evaluate side-chains 474 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 406 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 222 THR 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 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 815 GLU Chi-restraints excluded: chain A residue 835 THR 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 92 LEU 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 242 THR 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 682 GLU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 804 THR 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 20 CYS 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 238 SER Chi-restraints excluded: chain C residue 300 MET 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 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 799 PHE 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 28 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 123 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 198 optimal weight: 0.0770 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 ASN A 955 HIS B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 415 ASN C 517 GLN C 520 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118109 restraints weight = 29084.199| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.95 r_work: 0.3234 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24080 Z= 0.118 Angle : 0.531 9.894 32717 Z= 0.268 Chirality : 0.039 0.174 3809 Planarity : 0.003 0.047 4219 Dihedral : 3.966 48.764 3324 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.42 % Allowed : 19.03 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3089 helix: 2.05 (0.12), residues: 1738 sheet: -0.46 (0.24), residues: 441 loop : 0.10 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 540 HIS 0.006 0.001 HIS C 955 PHE 0.012 0.001 PHE B 553 TYR 0.014 0.001 TYR B 597 ARG 0.004 0.000 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1550) hydrogen bonds : angle 4.42339 ( 4743) covalent geometry : bond 0.00265 (24080) covalent geometry : angle 0.53078 (32717) *********************** 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 518 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 432 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7583 (ttm110) REVERT: A 102 GLU cc_start: 0.8397 (tp30) cc_final: 0.8077 (tp30) REVERT: A 108 GLN cc_start: 0.7945 (tp40) cc_final: 0.7209 (tp40) REVERT: A 182 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 254 ASN cc_start: 0.7224 (m-40) cc_final: 0.6967 (m110) REVERT: A 312 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 429 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6624 (tp30) REVERT: A 498 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7427 (mtmm) REVERT: A 524 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 536 ARG cc_start: 0.7464 (tpt-90) cc_final: 0.6770 (mmm-85) REVERT: A 538 LEU cc_start: 0.7450 (tp) cc_final: 0.6637 (mp) REVERT: A 539 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6852 (ptm160) REVERT: A 581 SER cc_start: 0.7652 (m) cc_final: 0.7369 (p) REVERT: A 656 GLN cc_start: 0.8305 (tt0) cc_final: 0.7770 (mm110) REVERT: A 749 GLN cc_start: 0.7836 (tt0) cc_final: 0.7389 (mt0) REVERT: A 806 ARG cc_start: 0.7978 (ptt-90) cc_final: 0.7587 (ptt90) REVERT: A 839 MET cc_start: 0.6943 (mmt) cc_final: 0.6401 (mmt) REVERT: A 953 LYS cc_start: 0.7808 (pttt) cc_final: 0.6947 (mtmm) REVERT: A 959 GLU cc_start: 0.7368 (tt0) cc_final: 0.6866 (mm-30) REVERT: B 70 THR cc_start: 0.8271 (m) cc_final: 0.7984 (p) REVERT: B 112 GLN cc_start: 0.7723 (tp40) cc_final: 0.7165 (mm-40) REVERT: B 124 ASN cc_start: 0.8498 (t0) cc_final: 0.8216 (m-40) REVERT: B 164 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: B 182 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: B 211 ASN cc_start: 0.7662 (t0) cc_final: 0.7255 (t0) REVERT: B 274 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8342 (mtmm) REVERT: B 359 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 423 GLU cc_start: 0.8053 (mp0) cc_final: 0.7501 (mt-10) REVERT: B 518 MET cc_start: 0.8202 (tmm) cc_final: 0.7863 (tmm) REVERT: B 525 ARG cc_start: 0.8543 (ttm110) cc_final: 0.6820 (ttp80) REVERT: B 595 LYS cc_start: 0.8574 (tttt) cc_final: 0.7976 (ttpt) REVERT: B 659 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 737 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8084 (mm) REVERT: B 806 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7598 (mtm110) REVERT: B 842 MET cc_start: 0.8477 (tpt) cc_final: 0.8256 (mmp) REVERT: B 860 MET cc_start: 0.7942 (ttp) cc_final: 0.7705 (tpp) REVERT: B 889 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 900 MET cc_start: 0.8665 (tpp) cc_final: 0.8300 (mmm) REVERT: B 976 SER cc_start: 0.8929 (t) cc_final: 0.8699 (m) REVERT: B 1013 ILE cc_start: 0.8829 (pt) cc_final: 0.8456 (tp) REVERT: B 1029 ARG cc_start: 0.8121 (tpm-80) cc_final: 0.7707 (tpt90) REVERT: C 87 GLN cc_start: 0.7874 (tt0) cc_final: 0.7192 (mm-40) REVERT: C 95 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7933 (mttm) REVERT: C 227 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8269 (ptpp) REVERT: C 274 LYS cc_start: 0.8581 (mtpt) cc_final: 0.7867 (mmtt) REVERT: C 323 TYR cc_start: 0.8945 (p90) cc_final: 0.8091 (p90) REVERT: C 533 ILE cc_start: 0.8568 (tt) cc_final: 0.8353 (tt) REVERT: C 539 ARG cc_start: 0.7853 (tpt90) cc_final: 0.7514 (tpt90) REVERT: C 543 ILE cc_start: 0.8140 (mt) cc_final: 0.7779 (mt) REVERT: C 547 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7507 (mp) REVERT: C 601 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7990 (mt-10) REVERT: C 897 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 900 MET cc_start: 0.8368 (mmm) cc_final: 0.7960 (mmm) REVERT: C 920 GLU cc_start: 0.6980 (tt0) cc_final: 0.6578 (tt0) REVERT: C 949 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7348 (mt-10) REVERT: C 953 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7224 (mmmt) outliers start: 86 outliers final: 55 residues processed: 496 average time/residue: 0.3445 time to fit residues: 269.2295 Evaluate side-chains 468 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE 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 256 ASP 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 815 GLU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 127 VAL 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 226 ASP Chi-restraints excluded: chain B residue 242 THR 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 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 737 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 804 THR 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 B residue 1005 MET Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 238 SER 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 547 LEU Chi-restraints excluded: chain C residue 558 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 41 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 248 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 535 HIS A 955 HIS B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113665 restraints weight = 29630.900| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.18 r_work: 0.3218 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24080 Z= 0.140 Angle : 0.547 10.208 32717 Z= 0.276 Chirality : 0.040 0.206 3809 Planarity : 0.003 0.047 4219 Dihedral : 3.962 48.576 3324 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.34 % Allowed : 19.11 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.15), residues: 3089 helix: 2.07 (0.12), residues: 1731 sheet: -0.57 (0.24), residues: 459 loop : 0.11 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 540 HIS 0.003 0.001 HIS C 955 PHE 0.012 0.001 PHE B 553 TYR 0.014 0.001 TYR B 597 ARG 0.005 0.000 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1550) hydrogen bonds : angle 4.44447 ( 4743) covalent geometry : bond 0.00331 (24080) covalent geometry : angle 0.54703 (32717) *********************** 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 511 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 427 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7939 (ttm110) REVERT: A 102 GLU cc_start: 0.8593 (tp30) cc_final: 0.8219 (tp30) REVERT: A 108 GLN cc_start: 0.8166 (tp40) cc_final: 0.7386 (tp40) REVERT: A 182 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: A 254 ASN cc_start: 0.7520 (m-40) cc_final: 0.7305 (m110) REVERT: A 312 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6920 (tm-30) REVERT: A 355 MET cc_start: 0.8056 (mmt) cc_final: 0.7661 (mmm) REVERT: A 429 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6879 (tp30) REVERT: A 498 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7508 (mtmm) REVERT: A 536 ARG cc_start: 0.7623 (tpt-90) cc_final: 0.6954 (mmm-85) REVERT: A 538 LEU cc_start: 0.7721 (tp) cc_final: 0.6857 (mp) REVERT: A 539 ARG cc_start: 0.7465 (ttt180) cc_final: 0.7135 (ptm160) REVERT: A 557 ARG cc_start: 0.7125 (tpp-160) cc_final: 0.6729 (tpp-160) REVERT: A 656 GLN cc_start: 0.8296 (tt0) cc_final: 0.7861 (mm110) REVERT: A 749 GLN cc_start: 0.7991 (tt0) cc_final: 0.7680 (mt0) REVERT: A 839 MET cc_start: 0.7201 (mmt) cc_final: 0.6746 (mmt) REVERT: A 953 LYS cc_start: 0.7736 (pttt) cc_final: 0.6809 (mtmm) REVERT: A 959 GLU cc_start: 0.7720 (tt0) cc_final: 0.7285 (mm-30) REVERT: B 70 THR cc_start: 0.8629 (m) cc_final: 0.8360 (p) REVERT: B 112 GLN cc_start: 0.7985 (tp40) cc_final: 0.7365 (mm-40) REVERT: B 115 MET cc_start: 0.7564 (tpp) cc_final: 0.7237 (mmm) REVERT: B 124 ASN cc_start: 0.8486 (t0) cc_final: 0.8179 (t0) REVERT: B 164 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 211 ASN cc_start: 0.7993 (t0) cc_final: 0.7724 (t0) REVERT: B 329 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 359 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 423 GLU cc_start: 0.8112 (mp0) cc_final: 0.7568 (mp0) REVERT: B 518 MET cc_start: 0.8287 (tmm) cc_final: 0.7930 (tmm) REVERT: B 525 ARG cc_start: 0.8753 (ttm110) cc_final: 0.7058 (ttp80) REVERT: B 595 LYS cc_start: 0.8765 (tttt) cc_final: 0.8175 (ttpt) REVERT: B 659 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 731 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: B 737 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 806 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7862 (mtm110) REVERT: B 842 MET cc_start: 0.8781 (tpt) cc_final: 0.8566 (mmp) REVERT: B 889 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 900 MET cc_start: 0.8737 (tpp) cc_final: 0.8405 (mmm) REVERT: B 976 SER cc_start: 0.9160 (t) cc_final: 0.8938 (m) REVERT: B 1013 ILE cc_start: 0.8875 (pt) cc_final: 0.8556 (tp) REVERT: C 87 GLN cc_start: 0.8146 (tt0) cc_final: 0.7672 (tp40) REVERT: C 227 LYS cc_start: 0.8575 (ptpp) cc_final: 0.8343 (ptpp) REVERT: C 274 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8172 (mmtt) REVERT: C 539 ARG cc_start: 0.8020 (tpt90) cc_final: 0.7226 (ptm160) REVERT: C 547 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7891 (mp) REVERT: C 860 MET cc_start: 0.8558 (mmm) cc_final: 0.7762 (tpt) REVERT: C 897 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 900 MET cc_start: 0.8567 (mmm) cc_final: 0.8222 (mmm) REVERT: C 920 GLU cc_start: 0.7378 (tt0) cc_final: 0.7042 (tt0) REVERT: C 949 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7483 (mt-10) REVERT: C 953 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7362 (mmmt) outliers start: 84 outliers final: 57 residues processed: 494 average time/residue: 0.4642 time to fit residues: 371.3053 Evaluate side-chains 464 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 398 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 405 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 666 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 127 VAL 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 242 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LEU 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 804 THR 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 844 SER 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 1005 MET 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 452 VAL 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 614 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 897 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 238 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 745 ASN A 955 HIS B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 716 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114342 restraints weight = 29549.606| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.17 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24080 Z= 0.130 Angle : 0.545 8.903 32717 Z= 0.275 Chirality : 0.040 0.216 3809 Planarity : 0.003 0.048 4219 Dihedral : 3.937 48.561 3324 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.38 % Allowed : 19.27 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3089 helix: 2.10 (0.12), residues: 1726 sheet: -0.50 (0.24), residues: 447 loop : 0.09 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 540 HIS 0.002 0.000 HIS A 600 PHE 0.013 0.001 PHE B 553 TYR 0.013 0.001 TYR B 597 ARG 0.005 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1550) hydrogen bonds : angle 4.39835 ( 4743) covalent geometry : bond 0.00305 (24080) covalent geometry : angle 0.54548 (32717) *********************** 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 517 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 432 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASN cc_start: 0.8800 (m-40) cc_final: 0.8415 (m110) REVERT: A 102 GLU cc_start: 0.8478 (tp30) cc_final: 0.8101 (tp30) REVERT: A 108 GLN cc_start: 0.8159 (tp40) cc_final: 0.7483 (tp40) REVERT: A 182 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 312 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 429 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6872 (tp30) REVERT: A 498 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7533 (mtmm) REVERT: A 536 ARG cc_start: 0.7613 (tpt-90) cc_final: 0.7036 (mmm-85) REVERT: A 538 LEU cc_start: 0.7729 (tp) cc_final: 0.6779 (mp) REVERT: A 539 ARG cc_start: 0.7326 (ttt180) cc_final: 0.6943 (ptm160) REVERT: A 557 ARG cc_start: 0.7216 (tpp-160) cc_final: 0.6805 (tpp-160) REVERT: A 656 GLN cc_start: 0.8259 (tt0) cc_final: 0.7867 (mm110) REVERT: A 749 GLN cc_start: 0.8024 (tt0) cc_final: 0.7703 (mt0) REVERT: A 839 MET cc_start: 0.7174 (mmt) cc_final: 0.6759 (mmt) REVERT: A 953 LYS cc_start: 0.7659 (pttt) cc_final: 0.6758 (mtmm) REVERT: A 959 GLU cc_start: 0.7668 (tt0) cc_final: 0.7295 (mm-30) REVERT: B 70 THR cc_start: 0.8674 (m) cc_final: 0.8395 (p) REVERT: B 112 GLN cc_start: 0.8007 (tp40) cc_final: 0.7396 (mm-40) REVERT: B 115 MET cc_start: 0.7479 (tpp) cc_final: 0.7188 (mmm) REVERT: B 124 ASN cc_start: 0.8415 (t0) cc_final: 0.8090 (t0) REVERT: B 164 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: B 182 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: B 329 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7708 (p) REVERT: B 359 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7547 (mt) REVERT: B 423 GLU cc_start: 0.7852 (mp0) cc_final: 0.7469 (mt-10) REVERT: B 518 MET cc_start: 0.8342 (tmm) cc_final: 0.7929 (tmm) REVERT: B 521 ARG cc_start: 0.7996 (ptp-170) cc_final: 0.7642 (ptp-170) REVERT: B 525 ARG cc_start: 0.8775 (ttm110) cc_final: 0.7093 (ttp80) REVERT: B 595 LYS cc_start: 0.8730 (tttt) cc_final: 0.8175 (ttpt) REVERT: B 659 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8073 (mt-10) REVERT: B 731 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7633 (mm-40) REVERT: B 737 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 806 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7861 (mtm110) REVERT: B 842 MET cc_start: 0.8790 (tpt) cc_final: 0.8588 (mmp) REVERT: B 889 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8825 (tp) REVERT: B 900 MET cc_start: 0.8670 (tpp) cc_final: 0.8321 (mmt) REVERT: B 976 SER cc_start: 0.9165 (t) cc_final: 0.8917 (m) REVERT: B 1013 ILE cc_start: 0.8870 (pt) cc_final: 0.8559 (tp) REVERT: C 87 GLN cc_start: 0.8255 (tt0) cc_final: 0.7722 (tp40) REVERT: C 156 ASP cc_start: 0.9035 (t0) cc_final: 0.8621 (t0) REVERT: C 274 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8174 (mmtt) REVERT: C 539 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7069 (ptm160) REVERT: C 547 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 860 MET cc_start: 0.8070 (mmm) cc_final: 0.7334 (tpt) REVERT: C 897 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7759 (t80) REVERT: C 900 MET cc_start: 0.8570 (mmm) cc_final: 0.8282 (mmm) REVERT: C 953 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7406 (mmmt) REVERT: C 966 ARG cc_start: 0.7451 (mmt180) cc_final: 0.6268 (ttp-110) REVERT: C 967 GLN cc_start: 0.7171 (mt0) cc_final: 0.6777 (mt0) REVERT: C 970 ARG cc_start: 0.8644 (ttt180) cc_final: 0.8308 (ttt90) outliers start: 85 outliers final: 60 residues processed: 500 average time/residue: 0.3410 time to fit residues: 271.8683 Evaluate side-chains 469 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 399 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 256 ASP 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 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 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL 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 164 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 TYR 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 242 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LEU 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 804 THR 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 844 SER 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 1005 MET 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 452 VAL 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 897 PHE 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 149 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 955 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 516 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112485 restraints weight = 29579.394| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.17 r_work: 0.3180 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.7921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24080 Z= 0.151 Angle : 0.566 9.633 32717 Z= 0.286 Chirality : 0.041 0.222 3809 Planarity : 0.004 0.049 4219 Dihedral : 3.975 47.758 3324 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.30 % Allowed : 19.55 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3089 helix: 2.06 (0.12), residues: 1727 sheet: -0.50 (0.24), residues: 455 loop : 0.03 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 540 HIS 0.002 0.001 HIS A 600 PHE 0.015 0.001 PHE B 946 TYR 0.016 0.001 TYR C 182 ARG 0.006 0.000 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1550) hydrogen bonds : angle 4.43759 ( 4743) covalent geometry : bond 0.00364 (24080) covalent geometry : angle 0.56623 (32717) *********************** 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 493 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 410 time to evaluate : 2.526 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8417 (tp30) cc_final: 0.8018 (tp30) REVERT: A 108 GLN cc_start: 0.8170 (tp40) cc_final: 0.7483 (tp40) REVERT: A 182 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 248 ASP cc_start: 0.8628 (t0) cc_final: 0.8421 (t70) REVERT: A 312 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 340 VAL cc_start: 0.6501 (t) cc_final: 0.5898 (m) REVERT: A 429 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6847 (tp30) REVERT: A 498 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7608 (mtmm) REVERT: A 536 ARG cc_start: 0.7577 (tpt-90) cc_final: 0.7004 (mmm-85) REVERT: A 538 LEU cc_start: 0.7937 (tp) cc_final: 0.6935 (mp) REVERT: A 539 ARG cc_start: 0.7361 (ttt180) cc_final: 0.7000 (ptm160) REVERT: A 557 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.6815 (tpp-160) REVERT: A 656 GLN cc_start: 0.8187 (tt0) cc_final: 0.7909 (mm110) REVERT: A 749 GLN cc_start: 0.8082 (tt0) cc_final: 0.7652 (mt0) REVERT: A 839 MET cc_start: 0.7201 (mmt) cc_final: 0.6874 (mmt) REVERT: A 953 LYS cc_start: 0.7679 (pttt) cc_final: 0.6821 (mtmm) REVERT: A 959 GLU cc_start: 0.7753 (tt0) cc_final: 0.7345 (mm-30) REVERT: B 70 THR cc_start: 0.8690 (m) cc_final: 0.8422 (p) REVERT: B 112 GLN cc_start: 0.8088 (tp40) cc_final: 0.7479 (mm-40) REVERT: B 115 MET cc_start: 0.7607 (tpp) cc_final: 0.7372 (mmm) REVERT: B 124 ASN cc_start: 0.8402 (t0) cc_final: 0.8060 (t0) REVERT: B 164 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: B 182 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: B 329 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7761 (p) REVERT: B 423 GLU cc_start: 0.7985 (mp0) cc_final: 0.7400 (mt-10) REVERT: B 518 MET cc_start: 0.8364 (tmm) cc_final: 0.7996 (tmm) REVERT: B 525 ARG cc_start: 0.8800 (ttm110) cc_final: 0.7152 (ttp80) REVERT: B 595 LYS cc_start: 0.8663 (tttt) cc_final: 0.8129 (ttpt) REVERT: B 659 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 731 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7114 (mm-40) REVERT: B 737 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 806 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7817 (mtm110) REVERT: B 889 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8859 (tp) REVERT: B 900 MET cc_start: 0.8663 (tpp) cc_final: 0.8359 (mmt) REVERT: B 976 SER cc_start: 0.9198 (t) cc_final: 0.8967 (m) REVERT: B 1013 ILE cc_start: 0.8887 (pt) cc_final: 0.8598 (tp) REVERT: C 87 GLN cc_start: 0.8252 (tt0) cc_final: 0.7697 (tp40) REVERT: C 274 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8115 (mmtt) REVERT: C 304 GLU cc_start: 0.8245 (pt0) cc_final: 0.8011 (tp30) REVERT: C 338 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7137 (mt-10) REVERT: C 539 ARG cc_start: 0.7847 (tpt90) cc_final: 0.7286 (ptm160) REVERT: C 796 MET cc_start: 0.8649 (mmm) cc_final: 0.8244 (mmm) REVERT: C 857 TRP cc_start: 0.7895 (m100) cc_final: 0.7649 (m100) REVERT: C 860 MET cc_start: 0.8313 (mmm) cc_final: 0.7388 (tpt) REVERT: C 897 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 900 MET cc_start: 0.8564 (mmm) cc_final: 0.8277 (mmm) REVERT: C 949 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7615 (mt-10) REVERT: C 952 GLN cc_start: 0.7957 (mt0) cc_final: 0.7630 (mt0) REVERT: C 953 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7139 (mttt) REVERT: C 966 ARG cc_start: 0.7555 (mmt180) cc_final: 0.6293 (ttp-110) REVERT: C 967 GLN cc_start: 0.7308 (mt0) cc_final: 0.6856 (mm-40) REVERT: C 970 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8239 (ttt90) outliers start: 83 outliers final: 68 residues processed: 477 average time/residue: 0.3519 time to fit residues: 271.0829 Evaluate side-chains 468 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 392 time to evaluate : 2.778 ------------------------------------------------------------------------------- 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 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 MET 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 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 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL 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 164 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 TYR 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 242 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 329 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 804 THR 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 844 SER 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 1005 MET 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 238 SER 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 516 ASN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 614 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 897 PHE 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 245 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 217 optimal weight: 0.0670 chunk 166 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 535 HIS ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 HIS B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114760 restraints weight = 29639.502| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.17 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24080 Z= 0.119 Angle : 0.556 9.543 32717 Z= 0.281 Chirality : 0.040 0.273 3809 Planarity : 0.003 0.046 4219 Dihedral : 3.935 48.885 3324 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.75 % Allowed : 20.46 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3089 helix: 2.08 (0.12), residues: 1728 sheet: -0.51 (0.24), residues: 464 loop : 0.10 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 540 HIS 0.003 0.001 HIS B 686 PHE 0.019 0.001 PHE B 946 TYR 0.023 0.001 TYR C 890 ARG 0.007 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1550) hydrogen bonds : angle 4.36743 ( 4743) covalent geometry : bond 0.00272 (24080) covalent geometry : angle 0.55582 (32717) ********************** 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 471 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 402 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8341 (tp30) cc_final: 0.7890 (tp30) REVERT: A 182 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 248 ASP cc_start: 0.8559 (t0) cc_final: 0.8350 (t70) REVERT: A 254 ASN cc_start: 0.7625 (m-40) cc_final: 0.6926 (m-40) REVERT: A 312 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 429 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6854 (tp30) REVERT: A 498 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7523 (mtmm) REVERT: A 536 ARG cc_start: 0.7585 (tpt-90) cc_final: 0.7032 (mmm-85) REVERT: A 538 LEU cc_start: 0.7945 (tp) cc_final: 0.6970 (mp) REVERT: A 539 ARG cc_start: 0.7406 (ttt180) cc_final: 0.7091 (ptm160) REVERT: A 557 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6849 (tpp-160) REVERT: A 656 GLN cc_start: 0.8238 (tt0) cc_final: 0.8030 (mm110) REVERT: A 749 GLN cc_start: 0.8010 (tt0) cc_final: 0.7614 (mt0) REVERT: A 839 MET cc_start: 0.7166 (mmt) cc_final: 0.6849 (mmt) REVERT: A 953 LYS cc_start: 0.7748 (pttt) cc_final: 0.6863 (mtmm) REVERT: A 959 GLU cc_start: 0.7686 (tt0) cc_final: 0.7293 (mm-30) REVERT: B 70 THR cc_start: 0.8635 (m) cc_final: 0.8383 (p) REVERT: B 112 GLN cc_start: 0.8087 (tp40) cc_final: 0.7822 (tp40) REVERT: B 124 ASN cc_start: 0.8379 (t0) cc_final: 0.8039 (m-40) REVERT: B 164 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: B 182 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: B 242 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 329 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7704 (p) REVERT: B 423 GLU cc_start: 0.7951 (mp0) cc_final: 0.7416 (mt-10) REVERT: B 518 MET cc_start: 0.8369 (tmm) cc_final: 0.7960 (tmm) REVERT: B 521 ARG cc_start: 0.7785 (ptp-170) cc_final: 0.7381 (ptp-170) REVERT: B 525 ARG cc_start: 0.8826 (ttm110) cc_final: 0.7159 (ttp80) REVERT: B 595 LYS cc_start: 0.8642 (tttt) cc_final: 0.8098 (ttpt) REVERT: B 731 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7559 (mm-40) REVERT: B 737 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B 976 SER cc_start: 0.9139 (t) cc_final: 0.8923 (m) REVERT: B 1013 ILE cc_start: 0.8865 (pt) cc_final: 0.8570 (tp) REVERT: C 68 ASN cc_start: 0.8309 (m-40) cc_final: 0.8099 (m110) REVERT: C 87 GLN cc_start: 0.8245 (tt0) cc_final: 0.7621 (mm-40) REVERT: C 156 ASP cc_start: 0.9040 (t0) cc_final: 0.8627 (t0) REVERT: C 274 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8099 (mmtt) REVERT: C 539 ARG cc_start: 0.7563 (tpt90) cc_final: 0.6991 (ptm160) REVERT: C 546 LEU cc_start: 0.8791 (mm) cc_final: 0.8574 (mp) REVERT: C 796 MET cc_start: 0.8616 (mmm) cc_final: 0.8204 (mmm) REVERT: C 857 TRP cc_start: 0.7889 (m100) cc_final: 0.7645 (m100) REVERT: C 860 MET cc_start: 0.8272 (mmm) cc_final: 0.7366 (tpt) REVERT: C 897 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 900 MET cc_start: 0.8520 (mmm) cc_final: 0.8239 (mmm) REVERT: C 952 GLN cc_start: 0.7931 (mt0) cc_final: 0.7660 (mt0) REVERT: C 953 LYS cc_start: 0.7653 (mtpp) cc_final: 0.7066 (mttt) REVERT: C 966 ARG cc_start: 0.7543 (mmt180) cc_final: 0.6276 (ttp-110) REVERT: C 967 GLN cc_start: 0.7210 (mt0) cc_final: 0.6825 (mm-40) REVERT: C 970 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8238 (ttt90) outliers start: 69 outliers final: 52 residues processed: 458 average time/residue: 0.3325 time to fit residues: 244.6476 Evaluate side-chains 444 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 384 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 ASP 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 483 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 983 VAL 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 164 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 TYR 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 242 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 329 THR Chi-restraints excluded: chain B residue 426 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 804 THR 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 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 238 SER 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 516 ASN Chi-restraints excluded: chain C residue 570 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 243 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 955 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109844 restraints weight = 29811.282| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.16 r_work: 0.3164 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24080 Z= 0.170 Angle : 0.592 10.556 32717 Z= 0.300 Chirality : 0.042 0.291 3809 Planarity : 0.004 0.058 4219 Dihedral : 4.000 46.297 3323 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.03 % Allowed : 20.58 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 3089 helix: 1.99 (0.12), residues: 1728 sheet: -0.49 (0.24), residues: 459 loop : 0.04 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 540 HIS 0.004 0.001 HIS A 600 PHE 0.024 0.001 PHE B 946 TYR 0.020 0.001 TYR B 597 ARG 0.005 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 1550) hydrogen bonds : angle 4.46883 ( 4743) covalent geometry : bond 0.00414 (24080) covalent geometry : angle 0.59199 (32717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14380.80 seconds wall clock time: 248 minutes 16.34 seconds (14896.34 seconds total)