Starting phenix.real_space_refine on Mon Feb 19 03:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_28848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_28848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_28848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_28848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2024/8f3e_28848.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.25, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.39 Conformation dependent library (CDL) restraints added in 4.3 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: 2.94 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: 10.51 Time building geometry restraints manager: 10.09 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: 97.41 - 104.72: 439 104.72 - 112.04: 12096 112.04 - 119.35: 7774 119.35 - 126.66: 12132 126.66 - 133.98: 276 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 2.520 nonbonded pdb=" OG SER A 561 " pdb=" OE1 GLU A 920 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP A 153 " pdb=" OH TYR A 182 " model vdw 2.229 2.440 nonbonded pdb=" OD1 ASP B 311 " pdb=" OH TYR B 323 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR B 46 " pdb=" OG1 THR B 128 " model vdw 2.244 2.440 ... (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 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.420 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 63.780 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.100 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.440 ------------------------------------------------------------------------------- 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= 0.210 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 *********************** 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 fitting. rotamer outliers: 73 poor density : 791 time to evaluate : 2.563 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: 0.3669 time to fit residues: 472.6187 Evaluate side-chains 483 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 471 time to evaluate : 2.535 ------------------------------------------------------------------------------- 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: 0.6980 chunk 234 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 157 optimal weight: 0.0980 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 105 GLN A 213 GLN A 235 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 724 GLN ** B 758 ASN ** 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 120 GLN C 123 GLN C 124 ASN C 152 GLN C 170 ASN C 218 GLN C 235 ASN C 241 GLN C 308 ASN ** 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 863 GLN ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 24080 Z= 0.221 Angle : 0.577 10.472 32717 Z= 0.298 Chirality : 0.041 0.170 3809 Planarity : 0.004 0.037 4219 Dihedral : 4.430 56.590 3339 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.07 % Allowed : 13.77 % Favored : 83.16 % 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: 1.69 (0.16), residues: 3089 helix: 2.11 (0.12), residues: 1724 sheet: -0.32 (0.24), residues: 462 loop : 0.08 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 540 HIS 0.009 0.001 HIS C 963 PHE 0.017 0.001 PHE C 511 TYR 0.016 0.001 TYR A 862 ARG 0.006 0.001 ARG A 813 *********************** 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 598 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 521 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.6263 (ppp) cc_final: 0.5906 (ppp) REVERT: B 596 TYR cc_start: 0.8295 (t80) cc_final: 0.8093 (t80) REVERT: C 76 MET cc_start: 0.6516 (mtm) cc_final: 0.6213 (ptp) REVERT: C 312 GLU cc_start: 0.6234 (tt0) cc_final: 0.5964 (tt0) REVERT: C 817 TYR cc_start: 0.7586 (t80) cc_final: 0.7340 (t80) outliers start: 77 outliers final: 41 residues processed: 570 average time/residue: 0.3277 time to fit residues: 300.2828 Evaluate side-chains 476 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 435 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 298 ASN 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 902 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 182 TYR 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 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 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 530 VAL 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 155 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 254 ASN A 360 GLN A 516 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 112 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 315 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN C 124 ASN C 170 ASN C 308 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24080 Z= 0.290 Angle : 0.628 14.923 32717 Z= 0.322 Chirality : 0.043 0.360 3809 Planarity : 0.004 0.065 4219 Dihedral : 4.483 59.934 3332 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.46 % Allowed : 15.57 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.15), residues: 3089 helix: 1.79 (0.12), residues: 1730 sheet: -0.39 (0.25), residues: 448 loop : 0.03 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 540 HIS 0.019 0.002 HIS A 535 PHE 0.027 0.002 PHE A 553 TYR 0.019 0.002 TYR A 875 ARG 0.011 0.001 ARG A 8 *********************** 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 647 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 535 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: A 570 MET cc_start: 0.6885 (ppp) cc_final: 0.6190 (ppp) REVERT: B 124 ASN cc_start: 0.6999 (t0) cc_final: 0.6709 (t0) REVERT: B 327 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 355 MET cc_start: 0.6710 (mmm) cc_final: 0.6395 (mtt) REVERT: B 359 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7347 (mt) REVERT: B 398 MET cc_start: 0.7541 (mtt) cc_final: 0.7308 (mtt) REVERT: B 1029 ARG cc_start: 0.6947 (tpm-80) cc_final: 0.6639 (tpt90) REVERT: C 270 MET cc_start: 0.8147 (mmm) cc_final: 0.7934 (mmm) REVERT: C 547 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7293 (mp) REVERT: C 659 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5734 (tt0) REVERT: C 860 MET cc_start: 0.6661 (mmm) cc_final: 0.6341 (tpt) outliers start: 112 outliers final: 56 residues processed: 614 average time/residue: 0.3376 time to fit residues: 327.5173 Evaluate side-chains 468 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 407 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 32 VAL 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 291 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 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 973 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 76 MET 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 242 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 344 LEU 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 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 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 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 922 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 MET 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 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 905 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 112 GLN A 254 ASN A 921 ASN A 926 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 237 GLN ** 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 120 GLN C 170 ASN C 315 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 517 GLN C 600 HIS ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24080 Z= 0.231 Angle : 0.563 11.270 32717 Z= 0.286 Chirality : 0.040 0.170 3809 Planarity : 0.004 0.041 4219 Dihedral : 4.074 47.873 3327 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.14 % Allowed : 18.07 % Favored : 77.79 % 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: 1.55 (0.15), residues: 3089 helix: 1.94 (0.12), residues: 1735 sheet: -0.34 (0.24), residues: 443 loop : 0.09 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 787 HIS 0.007 0.001 HIS C 963 PHE 0.021 0.001 PHE A 4 TYR 0.023 0.002 TYR C 182 ARG 0.009 0.001 ARG A 8 *********************** 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 580 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 476 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: A 270 MET cc_start: 0.7872 (mmm) cc_final: 0.7652 (mmm) REVERT: B 116 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7246 (mmm160) REVERT: B 164 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5613 (m-30) REVERT: B 182 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: B 327 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 359 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7312 (mt) REVERT: B 518 MET cc_start: 0.5902 (tmm) cc_final: 0.5682 (tmm) REVERT: B 976 SER cc_start: 0.8546 (t) cc_final: 0.8211 (m) REVERT: B 1029 ARG cc_start: 0.7149 (tpm-80) cc_final: 0.6762 (tpt90) REVERT: C 184 MET cc_start: 0.7907 (tpp) cc_final: 0.7632 (tpt) REVERT: C 270 MET cc_start: 0.7953 (mmm) cc_final: 0.7697 (mmm) REVERT: C 547 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7636 (mp) REVERT: C 860 MET cc_start: 0.7037 (tmm) cc_final: 0.6636 (tpt) REVERT: C 897 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 899 VAL cc_start: 0.8470 (t) cc_final: 0.8165 (t) outliers start: 104 outliers final: 55 residues processed: 551 average time/residue: 0.3315 time to fit residues: 292.6310 Evaluate side-chains 471 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 409 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 132 THR 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 815 GLU Chi-restraints excluded: chain A residue 878 SER 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 14 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 233 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 327 TYR 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 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 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 922 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 533 ILE 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 897 PHE Chi-restraints excluded: chain C residue 905 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN C 415 ASN C 437 GLN C 516 ASN C 592 GLN C 951 ASN C 963 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24080 Z= 0.222 Angle : 0.537 11.198 32717 Z= 0.273 Chirality : 0.040 0.166 3809 Planarity : 0.003 0.045 4219 Dihedral : 3.999 47.532 3326 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.02 % Allowed : 19.35 % Favored : 76.63 % 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: 2.01 (0.12), residues: 1735 sheet: -0.43 (0.24), residues: 453 loop : 0.10 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 540 HIS 0.006 0.001 HIS C 955 PHE 0.019 0.001 PHE A 4 TYR 0.017 0.001 TYR A 875 ARG 0.005 0.000 ARG C 778 *********************** 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 545 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 444 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: A 270 MET cc_start: 0.7852 (mmm) cc_final: 0.7592 (mmm) REVERT: A 950 MET cc_start: 0.7658 (mtm) cc_final: 0.7436 (mtm) REVERT: B 164 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: B 182 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: B 359 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7174 (mt) REVERT: B 452 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (t) REVERT: B 518 MET cc_start: 0.5906 (tmm) cc_final: 0.5564 (tmm) REVERT: B 1029 ARG cc_start: 0.7196 (tpm-80) cc_final: 0.6972 (tpt90) REVERT: C 184 MET cc_start: 0.7765 (tpp) cc_final: 0.7496 (tpt) REVERT: C 547 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7566 (mp) REVERT: C 860 MET cc_start: 0.7154 (tmm) cc_final: 0.6726 (tpt) REVERT: C 897 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7320 (t80) outliers start: 101 outliers final: 72 residues processed: 520 average time/residue: 0.3297 time to fit residues: 273.9286 Evaluate side-chains 482 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 403 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 256 ASP 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 879 LEU 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 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 306 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 922 ASP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 516 ASN Chi-restraints excluded: chain C residue 533 ILE 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 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 784 ILE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 254 ASN A 360 GLN A 656 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 926 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** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 516 ASN C 517 GLN C 967 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24080 Z= 0.205 Angle : 0.540 10.380 32717 Z= 0.272 Chirality : 0.040 0.267 3809 Planarity : 0.003 0.047 4219 Dihedral : 3.968 48.056 3326 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.62 % Allowed : 20.30 % Favored : 76.07 % 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: 1.61 (0.15), residues: 3089 helix: 2.05 (0.12), residues: 1735 sheet: -0.51 (0.24), residues: 454 loop : 0.12 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 857 HIS 0.005 0.001 HIS C 955 PHE 0.015 0.001 PHE A 4 TYR 0.013 0.001 TYR A 323 ARG 0.005 0.000 ARG A 557 *********************** 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 512 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 421 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: A 270 MET cc_start: 0.7830 (mmm) cc_final: 0.7590 (mmm) REVERT: A 538 LEU cc_start: 0.7464 (tp) cc_final: 0.7217 (mp) REVERT: B 164 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5646 (m-30) REVERT: B 182 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8263 (m-10) REVERT: B 359 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7080 (mt) REVERT: B 423 GLU cc_start: 0.6776 (mp0) cc_final: 0.6520 (mt-10) REVERT: B 518 MET cc_start: 0.5915 (tmm) cc_final: 0.5555 (tmm) REVERT: C 184 MET cc_start: 0.7835 (tpp) cc_final: 0.7554 (tpt) REVERT: C 547 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7666 (mp) REVERT: C 897 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7284 (t80) outliers start: 91 outliers final: 66 residues processed: 490 average time/residue: 0.3353 time to fit residues: 261.2363 Evaluate side-chains 472 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 400 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 80 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 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 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 14 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 233 THR Chi-restraints excluded: chain B residue 242 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 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 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU 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 180 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 LEU 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 784 ILE Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 254 ASN A 360 GLN A 516 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 120 GLN C 516 ASN C 517 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24080 Z= 0.210 Angle : 0.545 11.387 32717 Z= 0.274 Chirality : 0.040 0.353 3809 Planarity : 0.003 0.040 4219 Dihedral : 3.981 48.189 3326 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.10 % Allowed : 19.90 % Favored : 76.00 % 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: 2.04 (0.12), residues: 1733 sheet: -0.44 (0.24), residues: 443 loop : 0.11 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 540 HIS 0.004 0.001 HIS C 955 PHE 0.016 0.001 PHE A 380 TYR 0.013 0.001 TYR C 182 ARG 0.008 0.000 ARG C 966 *********************** 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 532 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 429 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: A 270 MET cc_start: 0.7817 (mmm) cc_final: 0.7308 (mmt) REVERT: A 538 LEU cc_start: 0.7466 (tp) cc_final: 0.7125 (mp) REVERT: A 799 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 998 HIS cc_start: 0.7637 (m170) cc_final: 0.7386 (m170) REVERT: B 164 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5574 (m-30) REVERT: B 182 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8275 (m-10) REVERT: B 359 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7089 (mt) REVERT: C 115 MET cc_start: 0.6421 (tpp) cc_final: 0.6117 (tpp) REVERT: C 184 MET cc_start: 0.7822 (tpp) cc_final: 0.7195 (tpt) REVERT: C 198 MET cc_start: 0.8473 (mtp) cc_final: 0.8051 (mtp) REVERT: C 547 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (mp) REVERT: C 897 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7154 (t80) REVERT: C 900 MET cc_start: 0.7361 (mmm) cc_final: 0.7149 (mmm) outliers start: 103 outliers final: 74 residues processed: 510 average time/residue: 0.3774 time to fit residues: 304.0428 Evaluate side-chains 471 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 390 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 132 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 298 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 426 THR 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 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 80 SER 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 225 VAL 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 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 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 603 ASP 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 804 THR Chi-restraints excluded: chain B residue 805 SER 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 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 376 LEU 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 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 784 ILE Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 535 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 81 GLN C 120 GLN C 170 ASN C 516 ASN C 520 ASN C 716 HIS C 745 ASN C 955 HIS C 967 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24080 Z= 0.196 Angle : 0.538 9.705 32717 Z= 0.271 Chirality : 0.039 0.195 3809 Planarity : 0.003 0.041 4219 Dihedral : 3.960 49.403 3326 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.90 % Allowed : 20.14 % Favored : 75.96 % 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: 1.69 (0.15), residues: 3089 helix: 2.08 (0.12), residues: 1733 sheet: -0.36 (0.24), residues: 440 loop : 0.14 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 540 HIS 0.002 0.001 HIS A 535 PHE 0.013 0.001 PHE A 4 TYR 0.023 0.001 TYR A 384 ARG 0.006 0.000 ARG B 813 *********************** 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 495 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 397 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: A 270 MET cc_start: 0.7780 (mmm) cc_final: 0.7313 (mmt) REVERT: A 287 SER cc_start: 0.8228 (m) cc_final: 0.7898 (t) REVERT: A 456 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7204 (ptt) REVERT: A 538 LEU cc_start: 0.7490 (tp) cc_final: 0.7173 (mp) REVERT: A 608 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7105 (t) REVERT: A 779 MET cc_start: 0.7693 (mmm) cc_final: 0.7296 (mmp) REVERT: A 986 MET cc_start: 0.7685 (ttm) cc_final: 0.7468 (ttm) REVERT: A 998 HIS cc_start: 0.7609 (m170) cc_final: 0.7378 (m170) REVERT: B 18 LEU cc_start: 0.8672 (mt) cc_final: 0.8460 (mt) REVERT: B 164 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5655 (m-30) REVERT: B 182 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: B 731 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7368 (mm-40) REVERT: C 115 MET cc_start: 0.6501 (tpp) cc_final: 0.6171 (tpp) REVERT: C 198 MET cc_start: 0.8448 (mtp) cc_final: 0.8060 (mtp) REVERT: C 547 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 897 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7049 (t80) REVERT: C 900 MET cc_start: 0.7292 (mmm) cc_final: 0.7090 (mmm) REVERT: C 970 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7142 (ttt180) outliers start: 98 outliers final: 70 residues processed: 472 average time/residue: 0.3370 time to fit residues: 254.6704 Evaluate side-chains 455 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 377 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 80 SER 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 336 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER 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 879 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 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 182 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL 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 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 581 SER Chi-restraints excluded: chain B residue 603 ASP 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 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 376 LEU 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 533 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 614 SER 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 780 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 535 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 516 ASN C 955 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.8034 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= 0.269 Angle : 0.578 13.040 32717 Z= 0.293 Chirality : 0.041 0.278 3809 Planarity : 0.004 0.048 4219 Dihedral : 4.066 47.088 3326 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.46 % Allowed : 20.34 % Favored : 76.19 % 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: 1.58 (0.15), residues: 3089 helix: 2.00 (0.12), residues: 1732 sheet: -0.45 (0.24), residues: 452 loop : 0.11 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 540 HIS 0.003 0.001 HIS A 691 PHE 0.013 0.001 PHE B 317 TYR 0.021 0.001 TYR A 384 ARG 0.006 0.001 ARG B 813 *********************** 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 475 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 388 time to evaluate : 2.625 Fit side-chains revert: symmetry clash REVERT: A 182 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: A 287 SER cc_start: 0.8372 (m) cc_final: 0.8068 (t) REVERT: A 456 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7225 (ptt) REVERT: A 538 LEU cc_start: 0.7658 (tp) cc_final: 0.7196 (mp) REVERT: A 608 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7282 (t) REVERT: A 799 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 18 LEU cc_start: 0.8644 (mt) cc_final: 0.8423 (mt) REVERT: B 132 THR cc_start: 0.7674 (t) cc_final: 0.7419 (t) REVERT: B 164 ASP cc_start: 0.5971 (m-30) cc_final: 0.5657 (m-30) REVERT: B 182 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: B 419 ILE cc_start: 0.8374 (mm) cc_final: 0.8131 (mt) REVERT: B 681 MET cc_start: 0.8293 (ttp) cc_final: 0.8066 (ttp) REVERT: B 731 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7374 (mm-40) REVERT: C 198 MET cc_start: 0.8459 (mtp) cc_final: 0.8109 (mtp) REVERT: C 897 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6970 (t80) outliers start: 87 outliers final: 71 residues processed: 457 average time/residue: 0.3329 time to fit residues: 242.5416 Evaluate side-chains 444 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 366 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 80 SER 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 298 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER 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 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL 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 426 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 614 SER 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 784 ILE Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 chunk 204 optimal weight: 7.9990 chunk 307 optimal weight: 2.9990 chunk 283 optimal weight: 0.0170 chunk 245 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 81 GLN C 120 GLN C 516 ASN C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.8197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24080 Z= 0.179 Angle : 0.551 11.924 32717 Z= 0.276 Chirality : 0.040 0.264 3809 Planarity : 0.003 0.053 4219 Dihedral : 4.006 49.286 3326 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.51 % Allowed : 21.70 % Favored : 75.80 % 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: 1.67 (0.15), residues: 3089 helix: 2.08 (0.12), residues: 1733 sheet: -0.46 (0.24), residues: 428 loop : 0.12 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 540 HIS 0.002 0.001 HIS A 535 PHE 0.014 0.001 PHE A 4 TYR 0.022 0.001 TYR C 157 ARG 0.005 0.000 ARG C 966 ********************** 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 463 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 400 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.6936 (tp40) cc_final: 0.6629 (tp40) REVERT: A 182 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: A 287 SER cc_start: 0.8262 (m) cc_final: 0.7992 (t) REVERT: A 438 ILE cc_start: 0.7894 (tt) cc_final: 0.7499 (tt) REVERT: A 456 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7147 (ptt) REVERT: A 538 LEU cc_start: 0.7635 (tp) cc_final: 0.7197 (mp) REVERT: A 608 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7275 (t) REVERT: B 78 MET cc_start: 0.8189 (ttp) cc_final: 0.7918 (mtm) REVERT: B 132 THR cc_start: 0.7683 (t) cc_final: 0.7441 (t) REVERT: B 164 ASP cc_start: 0.6117 (m-30) cc_final: 0.5831 (m-30) REVERT: B 182 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8203 (m-10) REVERT: B 731 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7410 (mm-40) REVERT: C 115 MET cc_start: 0.6594 (tpp) cc_final: 0.6374 (tpp) REVERT: C 198 MET cc_start: 0.8442 (mtp) cc_final: 0.7997 (mtp) REVERT: C 796 MET cc_start: 0.7783 (mmm) cc_final: 0.7505 (mmm) REVERT: C 897 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6922 (t80) outliers start: 63 outliers final: 55 residues processed: 449 average time/residue: 0.3432 time to fit residues: 244.9459 Evaluate side-chains 441 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 380 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER 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 298 ASN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 LEU 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 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 603 ASP 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 804 THR Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 81 GLN 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 516 ASN Chi-restraints excluded: chain C residue 533 ILE 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 784 ILE Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 897 PHE Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 437 GLN C 516 ASN C 955 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115499 restraints weight = 29378.767| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.95 r_work: 0.3225 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24080 Z= 0.199 Angle : 0.557 11.594 32717 Z= 0.279 Chirality : 0.040 0.292 3809 Planarity : 0.003 0.054 4219 Dihedral : 3.967 49.203 3326 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.95 % Allowed : 21.38 % Favored : 75.68 % 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: 1.66 (0.15), residues: 3089 helix: 2.09 (0.12), residues: 1733 sheet: -0.47 (0.25), residues: 428 loop : 0.10 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 540 HIS 0.005 0.001 HIS A 600 PHE 0.030 0.001 PHE C 946 TYR 0.031 0.001 TYR C 157 ARG 0.007 0.000 ARG C 966 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.98 seconds wall clock time: 113 minutes 55.63 seconds (6835.63 seconds total)