Starting phenix.real_space_refine (version: dev) on Fri Feb 24 19:01:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2023/8f3e_28848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2023/8f3e_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_2023/8f3e_28848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2023/8f3e_28848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2023/8f3e_28848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3e_28848/02_2023/8f3e_28848.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 13.07, per 1000 atoms: 0.55 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: 10.27 Conformation dependent library (CDL) restraints added in 3.4 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: 1.85 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: 11.39 Time building geometry restraints manager: 10.89 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.470 Check model and map are aligned: 0.350 Process input model: 65.170 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 % 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 *********************** 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 : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 12 residues processed: 847 average time/residue: 0.3710 time to fit residues: 478.0172 Evaluate side-chains 482 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 470 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2062 time to fit residues: 8.1370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 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 726 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: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.138 24080 Z= 0.213 Angle : 0.571 10.545 32717 Z= 0.294 Chirality : 0.041 0.165 3809 Planarity : 0.004 0.041 4219 Dihedral : 3.764 16.257 3320 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.12), residues: 1727 sheet: -0.31 (0.25), residues: 451 loop : 0.06 (0.21), residues: 911 *********************** 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 581 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 512 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 35 residues processed: 553 average time/residue: 0.3397 time to fit residues: 301.8357 Evaluate side-chains 469 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 434 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2267 time to fit residues: 18.2468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 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 315 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN C 124 ASN C 308 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 HIS C 967 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 24080 Z= 0.292 Angle : 0.628 17.040 32717 Z= 0.322 Chirality : 0.043 0.320 3809 Planarity : 0.004 0.081 4219 Dihedral : 3.978 22.135 3320 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.15), residues: 3089 helix: 1.86 (0.12), residues: 1729 sheet: -0.37 (0.25), residues: 440 loop : 0.05 (0.21), residues: 920 *********************** 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 613 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 534 time to evaluate : 2.846 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 32 residues processed: 586 average time/residue: 0.3526 time to fit residues: 326.9649 Evaluate side-chains 448 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 416 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2195 time to fit residues: 16.9685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 254 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 517 GLN C 600 HIS C 684 GLN C 686 HIS ** C 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 24080 Z= 0.246 Angle : 0.567 11.035 32717 Z= 0.289 Chirality : 0.041 0.161 3809 Planarity : 0.004 0.043 4219 Dihedral : 3.870 20.775 3320 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3089 helix: 1.95 (0.12), residues: 1736 sheet: -0.30 (0.25), residues: 432 loop : 0.04 (0.21), residues: 921 *********************** 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 557 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 482 time to evaluate : 2.638 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 38 residues processed: 533 average time/residue: 0.3569 time to fit residues: 302.8977 Evaluate side-chains 451 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 413 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2288 time to fit residues: 19.4463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 B 81 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 237 GLN B 308 ASN B 315 GLN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN C 517 GLN C 592 GLN C 686 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 24080 Z= 0.355 Angle : 0.628 11.837 32717 Z= 0.322 Chirality : 0.043 0.161 3809 Planarity : 0.004 0.040 4219 Dihedral : 4.109 20.556 3320 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.91 % 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: 1.20 (0.15), residues: 3089 helix: 1.73 (0.12), residues: 1736 sheet: -0.64 (0.24), residues: 452 loop : -0.15 (0.21), residues: 901 *********************** 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 522 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 449 time to evaluate : 3.032 Fit side-chains outliers start: 73 outliers final: 44 residues processed: 501 average time/residue: 0.3760 time to fit residues: 298.1956 Evaluate side-chains 428 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 384 time to evaluate : 2.612 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2274 time to fit residues: 22.3878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 656 GLN A 708 ASN A 749 GLN ** 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 170 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN C 955 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24080 Z= 0.206 Angle : 0.550 10.297 32717 Z= 0.280 Chirality : 0.040 0.172 3809 Planarity : 0.004 0.040 4219 Dihedral : 3.932 18.924 3320 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.19 % 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: 1.44 (0.15), residues: 3089 helix: 1.94 (0.12), residues: 1735 sheet: -0.60 (0.24), residues: 448 loop : -0.04 (0.21), residues: 906 *********************** 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 453 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 423 time to evaluate : 2.880 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 445 average time/residue: 0.3719 time to fit residues: 263.0758 Evaluate side-chains 390 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 376 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2319 time to fit residues: 9.7351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 251 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 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 535 HIS A 926 GLN ** B 108 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24080 Z= 0.207 Angle : 0.547 8.777 32717 Z= 0.278 Chirality : 0.040 0.187 3809 Planarity : 0.003 0.037 4219 Dihedral : 3.891 20.881 3320 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.07 % 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: 1.49 (0.15), residues: 3089 helix: 2.00 (0.12), residues: 1733 sheet: -0.60 (0.24), residues: 438 loop : -0.05 (0.21), residues: 918 *********************** 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 440 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 413 time to evaluate : 2.541 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 432 average time/residue: 0.3646 time to fit residues: 249.5750 Evaluate side-chains 394 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 380 time to evaluate : 2.493 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2420 time to fit residues: 10.0834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** 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 437 GLN C 955 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24080 Z= 0.190 Angle : 0.545 8.461 32717 Z= 0.277 Chirality : 0.040 0.262 3809 Planarity : 0.003 0.037 4219 Dihedral : 3.878 20.935 3320 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.80 % 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: 1.56 (0.15), residues: 3089 helix: 2.05 (0.12), residues: 1732 sheet: -0.54 (0.24), residues: 445 loop : -0.02 (0.21), residues: 912 *********************** 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 423 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 403 time to evaluate : 2.861 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 416 average time/residue: 0.3643 time to fit residues: 240.5339 Evaluate side-chains 384 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 375 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2611 time to fit residues: 8.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 260 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 217 optimal weight: 0.0870 chunk 85 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS ** 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 254 ASN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN C 955 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.8159 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= 0.184 Angle : 0.549 9.808 32717 Z= 0.277 Chirality : 0.040 0.231 3809 Planarity : 0.003 0.038 4219 Dihedral : 3.828 19.619 3320 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.56 % 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: 2.09 (0.12), residues: 1734 sheet: -0.52 (0.24), residues: 438 loop : -0.01 (0.21), residues: 917 *********************** 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 410 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 396 time to evaluate : 2.897 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 404 average time/residue: 0.3939 time to fit residues: 257.6676 Evaluate side-chains 382 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 374 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2649 time to fit residues: 8.0120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 204 optimal weight: 0.1980 chunk 307 optimal weight: 2.9990 chunk 283 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 254 ASN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.8227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24080 Z= 0.183 Angle : 0.547 10.196 32717 Z= 0.276 Chirality : 0.040 0.173 3809 Planarity : 0.003 0.038 4219 Dihedral : 3.789 19.283 3320 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3089 helix: 2.11 (0.12), residues: 1734 sheet: -0.47 (0.24), residues: 440 loop : 0.00 (0.21), residues: 915 ********************** 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 398 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 389 time to evaluate : 2.771 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 394 average time/residue: 0.3603 time to fit residues: 227.7416 Evaluate side-chains 377 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 373 time to evaluate : 2.780 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2406 time to fit residues: 5.6169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 252 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 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 112 GLN A 535 HIS ** 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 254 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117538 restraints weight = 29168.898| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.94 r_work: 0.3250 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24080 Z= 0.178 Angle : 0.547 10.511 32717 Z= 0.276 Chirality : 0.039 0.173 3809 Planarity : 0.003 0.037 4219 Dihedral : 3.742 19.095 3320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.36 % 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: 2.13 (0.12), residues: 1733 sheet: -0.43 (0.24), residues: 438 loop : 0.06 (0.21), residues: 918 =============================================================================== Job complete usr+sys time: 6240.03 seconds wall clock time: 113 minutes 24.89 seconds (6804.89 seconds total)