Starting phenix.real_space_refine on Sun Sep 29 04:30:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/09_2024/8j7o_36044_neut_trim.cif" } resolution = 3.83 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= -0.002 sd= 0.035 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 148 5.16 5 C 13448 2.51 5 N 3632 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "B" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "C" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "E" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.52, per 1000 atoms: 0.64 Number of scatterers: 21168 At special positions: 0 Unit cell: (161.391, 106.496, 133.944, 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 148 16.00 O 3940 8.00 N 3632 7.00 C 13448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.8 seconds 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 16 sheets defined 50.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 540 through 559 removed outlier: 3.815A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.569A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 610 through 619 removed outlier: 3.664A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 655 through 669 removed outlier: 3.569A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 809 through 818 Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 7.345A pdb=" N CYS A 850 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR A 851 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 881 Processing helix chain 'A' and resid 883 through 885 No H-bonds generated for 'chain 'A' and resid 883 through 885' Processing helix chain 'A' and resid 886 through 902 Processing helix chain 'A' and resid 909 through 925 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 962 through 969 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER A 981 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1034 through 1041 Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.816A pdb=" N ILE B 544 " --> pdb=" O GLY B 540 " (cutoff:3.500A) Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 610 through 619 removed outlier: 3.663A pdb=" N MET B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 Processing helix chain 'B' and resid 655 through 669 removed outlier: 3.570A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 719 through 733 Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'B' and resid 778 through 789 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 809 through 818 Processing helix chain 'B' and resid 827 through 845 removed outlier: 3.601A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 853 removed outlier: 7.345A pdb=" N CYS B 850 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR B 851 " --> pdb=" O PHE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 Processing helix chain 'B' and resid 883 through 885 No H-bonds generated for 'chain 'B' and resid 883 through 885' Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'B' and resid 909 through 925 Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 962 through 969 Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER B 981 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1034 through 1041 Processing helix chain 'C' and resid 495 through 511 Processing helix chain 'C' and resid 540 through 559 removed outlier: 3.817A pdb=" N ILE C 544 " --> pdb=" O GLY C 540 " (cutoff:3.500A) Proline residue: C 550 - end of helix Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Proline residue: C 592 - end of helix Processing helix chain 'C' and resid 610 through 619 removed outlier: 3.663A pdb=" N MET C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 Processing helix chain 'C' and resid 655 through 669 removed outlier: 3.569A pdb=" N VAL C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 719 through 733 Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 778 through 789 Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 809 through 818 Processing helix chain 'C' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 853 removed outlier: 7.346A pdb=" N CYS C 850 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR C 851 " --> pdb=" O PHE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 Processing helix chain 'C' and resid 867 through 881 Processing helix chain 'C' and resid 883 through 885 No H-bonds generated for 'chain 'C' and resid 883 through 885' Processing helix chain 'C' and resid 886 through 902 Processing helix chain 'C' and resid 909 through 925 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 962 through 969 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER C 981 " --> pdb=" O PRO C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 999 Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1029 through 1033 Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'C' and resid 1091 through 1096 removed outlier: 4.215A pdb=" N MET C1095 " --> pdb=" O ASP C1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 511 Processing helix chain 'E' and resid 540 through 559 removed outlier: 3.817A pdb=" N ILE E 544 " --> pdb=" O GLY E 540 " (cutoff:3.500A) Proline residue: E 550 - end of helix Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE E 590 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Proline residue: E 592 - end of helix Processing helix chain 'E' and resid 610 through 619 removed outlier: 3.662A pdb=" N MET E 616 " --> pdb=" O PHE E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 634 Processing helix chain 'E' and resid 655 through 669 removed outlier: 3.570A pdb=" N VAL E 659 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 696 Processing helix chain 'E' and resid 719 through 733 Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'E' and resid 778 through 789 Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 809 through 818 Processing helix chain 'E' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU E 844 " --> pdb=" O GLY E 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR E 845 " --> pdb=" O ALA E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 853 removed outlier: 7.346A pdb=" N CYS E 850 " --> pdb=" O ALA E 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR E 851 " --> pdb=" O PHE E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 860 through 865 Processing helix chain 'E' and resid 867 through 881 Processing helix chain 'E' and resid 883 through 885 No H-bonds generated for 'chain 'E' and resid 883 through 885' Processing helix chain 'E' and resid 886 through 902 Processing helix chain 'E' and resid 909 through 925 Processing helix chain 'E' and resid 927 through 934 Processing helix chain 'E' and resid 941 through 950 Processing helix chain 'E' and resid 962 through 969 Processing helix chain 'E' and resid 977 through 982 removed outlier: 3.804A pdb=" N SER E 981 " --> pdb=" O PRO E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 999 Processing helix chain 'E' and resid 1003 through 1013 Processing helix chain 'E' and resid 1013 through 1028 Processing helix chain 'E' and resid 1029 through 1033 Processing helix chain 'E' and resid 1034 through 1041 Processing helix chain 'E' and resid 1091 through 1096 removed outlier: 4.385A pdb=" N MET E1095 " --> pdb=" O ASP E1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.872A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 674 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 703 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 676 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 705 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET A 641 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 677 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 643 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1053 removed outlier: 7.067A pdb=" N LYS A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN A1075 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A1068 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A1073 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 6.948A pdb=" N ILE A1112 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A1174 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A1160 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A1139 " --> pdb=" O THR A1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1149 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.938A pdb=" N LEU B 565 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.326A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N GLY B 608 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE B 674 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 703 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 676 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER B 705 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1053 removed outlier: 6.251A pdb=" N GLU B1047 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA B1062 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B1049 " --> pdb=" O ILE B1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B1060 " --> pdb=" O GLU B1049 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU B1051 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B1058 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B1053 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA B1062 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B1075 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B1068 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B1073 " --> pdb=" O LEU B1068 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1111 through 1113 removed outlier: 6.949A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B1174 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL B1160 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B1176 " --> pdb=" O ARG B1158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR B1147 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B1139 " --> pdb=" O THR B1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B1149 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 564 through 567 removed outlier: 8.382A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 674 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 703 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 676 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER C 705 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL C 796 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET C 566 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1047 through 1053 removed outlier: 6.252A pdb=" N GLU C1047 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA C1062 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU C1049 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C1060 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU C1051 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C1058 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C1053 " --> pdb=" O LYS C1056 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN C1075 " --> pdb=" O SER C1066 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C1068 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C1073 " --> pdb=" O LEU C1068 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1111 through 1113 removed outlier: 6.950A pdb=" N ILE C1112 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C1174 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C1160 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 603 through 604 removed outlier: 4.266A pdb=" N SER E 603 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 564 " --> pdb=" O VAL E 794 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL E 796 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N MET E 566 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 738 " --> pdb=" O HIS E 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS E 771 " --> pdb=" O LEU E 738 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 740 " --> pdb=" O HIS E 771 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 674 " --> pdb=" O GLU E 701 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA E 703 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 676 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER E 705 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET E 641 " --> pdb=" O ARG E 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE E 677 " --> pdb=" O MET E 641 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 643 " --> pdb=" O PHE E 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1047 through 1053 removed outlier: 6.252A pdb=" N GLU E1047 " --> pdb=" O ALA E1062 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA E1062 " --> pdb=" O GLU E1047 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU E1049 " --> pdb=" O ILE E1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E1060 " --> pdb=" O GLU E1049 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU E1051 " --> pdb=" O LEU E1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E1058 " --> pdb=" O GLU E1051 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU E1053 " --> pdb=" O LYS E1056 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA E1062 " --> pdb=" O GLU E1079 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU E1079 " --> pdb=" O ALA E1062 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E1075 " --> pdb=" O SER E1066 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU E1068 " --> pdb=" O GLN E1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN E1073 " --> pdb=" O LEU E1068 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1111 through 1113 removed outlier: 6.948A pdb=" N ILE E1112 " --> pdb=" O ILE E1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E1174 " --> pdb=" O VAL E1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL E1160 " --> pdb=" O ILE E1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E1176 " --> pdb=" O ARG E1158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1146 through 1150 removed outlier: 6.315A pdb=" N THR E1147 " --> pdb=" O VAL E1139 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL E1139 " --> pdb=" O THR E1147 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL E1149 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU E1137 " --> pdb=" O ILE E1123 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE E1123 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL E1139 " --> pdb=" O ILE E1121 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2808 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: 7.39 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3903 1.32 - 1.45: 5039 1.45 - 1.57: 12442 1.57 - 1.70: 0 1.70 - 1.83: 264 Bond restraints: 21648 Sorted by residual: bond pdb=" C LYS A1144 " pdb=" N MET A1145 " ideal model delta sigma weight residual 1.332 1.436 -0.103 1.40e-02 5.10e+03 5.46e+01 bond pdb=" C LYS C1144 " pdb=" N MET C1145 " ideal model delta sigma weight residual 1.332 1.436 -0.103 1.40e-02 5.10e+03 5.42e+01 bond pdb=" C LYS B1144 " pdb=" N MET B1145 " ideal model delta sigma weight residual 1.332 1.435 -0.103 1.40e-02 5.10e+03 5.37e+01 bond pdb=" C LYS E1144 " pdb=" N MET E1145 " ideal model delta sigma weight residual 1.332 1.434 -0.102 1.40e-02 5.10e+03 5.31e+01 bond pdb=" CA PRO E 983 " pdb=" C PRO E 983 " ideal model delta sigma weight residual 1.514 1.540 -0.025 5.50e-03 3.31e+04 2.13e+01 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 27178 2.90 - 5.79: 2091 5.79 - 8.69: 63 8.69 - 11.58: 10 11.58 - 14.48: 6 Bond angle restraints: 29348 Sorted by residual: angle pdb=" N ALA C 573 " pdb=" CA ALA C 573 " pdb=" C ALA C 573 " ideal model delta sigma weight residual 113.12 100.75 12.37 1.25e+00 6.40e-01 9.80e+01 angle pdb=" N GLY A 608 " pdb=" CA GLY A 608 " pdb=" C GLY A 608 " ideal model delta sigma weight residual 112.14 124.48 -12.34 1.29e+00 6.01e-01 9.16e+01 angle pdb=" N ALA B 573 " pdb=" CA ALA B 573 " pdb=" C ALA B 573 " ideal model delta sigma weight residual 113.12 102.22 10.90 1.25e+00 6.40e-01 7.60e+01 angle pdb=" N ALA A 573 " pdb=" CA ALA A 573 " pdb=" C ALA A 573 " ideal model delta sigma weight residual 113.12 102.74 10.38 1.25e+00 6.40e-01 6.89e+01 angle pdb=" N GLY A 609 " pdb=" CA GLY A 609 " pdb=" C GLY A 609 " ideal model delta sigma weight residual 111.02 125.50 -14.48 1.86e+00 2.89e-01 6.06e+01 ... (remaining 29343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 12207 17.21 - 34.42: 726 34.42 - 51.63: 175 51.63 - 68.84: 69 68.84 - 86.04: 11 Dihedral angle restraints: 13188 sinusoidal: 5316 harmonic: 7872 Sorted by residual: dihedral pdb=" CA PHE B1078 " pdb=" C PHE B1078 " pdb=" N GLU B1079 " pdb=" CA GLU B1079 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE E1078 " pdb=" C PHE E1078 " pdb=" N GLU E1079 " pdb=" CA GLU E1079 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA PHE A1078 " pdb=" C PHE A1078 " pdb=" N GLU A1079 " pdb=" CA GLU A1079 " ideal model delta harmonic sigma weight residual 180.00 154.94 25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 13185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2340 0.093 - 0.185: 825 0.185 - 0.278: 97 0.278 - 0.370: 10 0.370 - 0.463: 4 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CA HIS A1101 " pdb=" N HIS A1101 " pdb=" C HIS A1101 " pdb=" CB HIS A1101 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA HIS C1101 " pdb=" N HIS C1101 " pdb=" C HIS C1101 " pdb=" CB HIS C1101 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA HIS B1101 " pdb=" N HIS B1101 " pdb=" C HIS B1101 " pdb=" CB HIS B1101 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 3273 not shown) Planarity restraints: 3848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 593 " -0.086 2.00e-02 2.50e+03 5.42e-02 5.88e+01 pdb=" CG TYR E 593 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 593 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR E 593 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 593 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR E 593 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR E 593 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR E 593 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 593 " -0.085 2.00e-02 2.50e+03 5.40e-02 5.82e+01 pdb=" CG TYR A 593 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 593 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 593 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 593 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A 593 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 593 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 593 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 593 " 0.086 2.00e-02 2.50e+03 5.40e-02 5.82e+01 pdb=" CG TYR B 593 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 593 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 593 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR B 593 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR B 593 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR B 593 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 593 " 0.097 2.00e-02 2.50e+03 ... (remaining 3845 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1124 2.76 - 3.30: 21169 3.30 - 3.83: 35312 3.83 - 4.37: 45528 4.37 - 4.90: 73738 Nonbonded interactions: 176871 Sorted by model distance: nonbonded pdb=" CD1 LEU A 904 " pdb=" O ILE A 905 " model vdw 2.226 3.460 nonbonded pdb=" CD1 LEU E 904 " pdb=" O ILE E 905 " model vdw 2.226 3.460 nonbonded pdb=" CD1 LEU B 904 " pdb=" O ILE B 905 " model vdw 2.226 3.460 nonbonded pdb=" CD1 LEU C 904 " pdb=" O ILE C 905 " model vdw 2.227 3.460 nonbonded pdb=" O ASN C 898 " pdb=" N ASP C 903 " model vdw 2.508 3.120 ... (remaining 176866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 48.290 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 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 : 0.012 0.103 21648 Z= 0.794 Angle : 1.603 14.477 29348 Z= 1.081 Chirality : 0.087 0.463 3276 Planarity : 0.012 0.125 3848 Dihedral : 12.721 86.045 8132 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Rotamer: Outliers : 2.65 % Allowed : 3.53 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.24 (0.15), residues: 2740 helix: 0.18 (0.13), residues: 1216 sheet: -0.50 (0.28), residues: 328 loop : -0.24 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP B 624 HIS 0.029 0.004 HIS B 771 PHE 0.053 0.010 PHE A 618 TYR 0.097 0.016 TYR E 593 ARG 0.018 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 354 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6718 (mp) REVERT: E 606 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6141 (p0) REVERT: E 783 MET cc_start: 0.7424 (mmp) cc_final: 0.7216 (mmp) REVERT: E 1166 MET cc_start: 0.2997 (ttt) cc_final: 0.2598 (mtp) outliers start: 60 outliers final: 12 residues processed: 400 average time/residue: 0.4229 time to fit residues: 245.6176 Evaluate side-chains 192 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN A 807 GLN A 998 HIS ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN A1135 GLN B 807 GLN B 998 HIS B1075 GLN B1135 GLN C 807 GLN C1075 GLN C1135 GLN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5766 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21648 Z= 0.254 Angle : 0.718 14.471 29348 Z= 0.365 Chirality : 0.045 0.195 3276 Planarity : 0.005 0.053 3848 Dihedral : 6.862 70.003 3077 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.68 % Allowed : 9.50 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.06 (0.16), residues: 2740 helix: 1.48 (0.15), residues: 1208 sheet: -0.26 (0.27), residues: 368 loop : 0.36 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 838 HIS 0.008 0.002 HIS C1161 PHE 0.029 0.002 PHE A1078 TYR 0.020 0.002 TYR E 503 ARG 0.013 0.001 ARG A1158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 MET cc_start: 0.8861 (mmp) cc_final: 0.8563 (mmp) REVERT: B 607 TRP cc_start: 0.5909 (OUTLIER) cc_final: 0.4873 (t60) REVERT: B 641 MET cc_start: 0.7619 (ptm) cc_final: 0.6994 (ptm) REVERT: B 810 MET cc_start: 0.7237 (tmm) cc_final: 0.6891 (tmm) REVERT: E 784 LEU cc_start: 0.7809 (pp) cc_final: 0.7318 (mm) REVERT: E 921 MET cc_start: 0.6914 (mmm) cc_final: 0.6475 (mmm) REVERT: E 1166 MET cc_start: 0.3144 (ttt) cc_final: 0.2752 (mtp) outliers start: 38 outliers final: 18 residues processed: 210 average time/residue: 0.3190 time to fit residues: 104.9201 Evaluate side-chains 169 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 220 optimal weight: 0.3980 chunk 245 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS B1135 GLN C 502 HIS C 560 HIS C 898 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS ** E 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 ASN E1073 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 21648 Z= 0.243 Angle : 0.680 15.012 29348 Z= 0.342 Chirality : 0.044 0.167 3276 Planarity : 0.005 0.054 3848 Dihedral : 6.145 58.949 3068 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.21 % Allowed : 9.76 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.73 (0.16), residues: 2740 helix: 1.16 (0.15), residues: 1220 sheet: -0.45 (0.26), residues: 392 loop : 0.26 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 607 HIS 0.006 0.001 HIS A 506 PHE 0.025 0.002 PHE C1078 TYR 0.022 0.002 TYR B 682 ARG 0.009 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 MET cc_start: 0.8842 (mmp) cc_final: 0.8620 (mmp) REVERT: A 810 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.4057 (tmm) REVERT: A 921 MET cc_start: 0.6538 (mmm) cc_final: 0.6156 (mpp) REVERT: A 1116 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4353 (ptp) REVERT: C 496 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5851 (mmm160) REVERT: C 641 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: C 743 MET cc_start: 0.4450 (tpt) cc_final: 0.4097 (tpt) REVERT: E 641 MET cc_start: 0.7190 (ppp) cc_final: 0.6961 (ppp) REVERT: E 1166 MET cc_start: 0.3449 (ttt) cc_final: 0.2868 (mtp) outliers start: 50 outliers final: 21 residues processed: 196 average time/residue: 0.3327 time to fit residues: 101.5487 Evaluate side-chains 169 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1073 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN B 502 HIS ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 GLN C 875 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN E 875 HIS E1073 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 21648 Z= 0.313 Angle : 0.765 18.176 29348 Z= 0.391 Chirality : 0.046 0.250 3276 Planarity : 0.006 0.071 3848 Dihedral : 5.751 58.886 3050 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.90 % Allowed : 11.53 % Favored : 86.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.44 % 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: 0.02 (0.16), residues: 2740 helix: 0.63 (0.14), residues: 1212 sheet: -0.67 (0.26), residues: 392 loop : -0.24 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 624 HIS 0.008 0.002 HIS A 875 PHE 0.030 0.002 PHE E1100 TYR 0.026 0.002 TYR C 682 ARG 0.025 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 881 MET cc_start: 0.7877 (mmt) cc_final: 0.7644 (mmp) REVERT: A 1116 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.4440 (ptp) REVERT: B 743 MET cc_start: 0.5121 (tpt) cc_final: 0.4889 (tpt) REVERT: B 804 MET cc_start: 0.6871 (mmp) cc_final: 0.6523 (mmp) REVERT: C 641 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7637 (ppp) REVERT: C 653 ASN cc_start: 0.6662 (OUTLIER) cc_final: 0.6412 (t0) REVERT: C 671 MET cc_start: 0.8101 (tpp) cc_final: 0.7899 (tpp) REVERT: C 743 MET cc_start: 0.5012 (tpt) cc_final: 0.4559 (tpt) REVERT: C 1077 PHE cc_start: 0.7313 (m-80) cc_final: 0.7039 (m-10) outliers start: 43 outliers final: 19 residues processed: 194 average time/residue: 0.3265 time to fit residues: 101.7446 Evaluate side-chains 169 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1090 LYS Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS A 647 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 ASN ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21648 Z= 0.249 Angle : 0.682 13.325 29348 Z= 0.341 Chirality : 0.044 0.155 3276 Planarity : 0.005 0.045 3848 Dihedral : 5.305 57.924 3042 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 12.19 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.11 (0.16), residues: 2740 helix: 0.74 (0.14), residues: 1208 sheet: -0.71 (0.26), residues: 392 loop : -0.19 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 838 HIS 0.011 0.001 HIS A1059 PHE 0.020 0.002 PHE B1078 TYR 0.014 0.002 TYR C 722 ARG 0.009 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 MET cc_start: 0.8514 (mmp) cc_final: 0.8292 (mmp) REVERT: A 881 MET cc_start: 0.7877 (mmt) cc_final: 0.7503 (mmp) REVERT: A 1116 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.3392 (ptp) REVERT: B 641 MET cc_start: 0.6605 (ptt) cc_final: 0.6052 (ptt) REVERT: B 686 MET cc_start: 0.8865 (mpp) cc_final: 0.8629 (mpp) REVERT: B 743 MET cc_start: 0.5295 (tpt) cc_final: 0.5088 (tpt) REVERT: B 804 MET cc_start: 0.6914 (mmp) cc_final: 0.6692 (mmp) REVERT: C 641 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7666 (ppp) REVERT: C 743 MET cc_start: 0.5172 (tpt) cc_final: 0.4603 (tpt) REVERT: C 804 MET cc_start: 0.7631 (mmp) cc_final: 0.7392 (mmp) REVERT: C 900 MET cc_start: 0.7372 (ttp) cc_final: 0.6975 (ttm) REVERT: C 1077 PHE cc_start: 0.7394 (m-80) cc_final: 0.7092 (m-10) REVERT: E 604 MET cc_start: 0.6910 (ppp) cc_final: 0.6673 (ppp) REVERT: E 921 MET cc_start: 0.7308 (mmm) cc_final: 0.6867 (mmm) REVERT: E 1166 MET cc_start: 0.2750 (ttt) cc_final: 0.2485 (ttt) outliers start: 36 outliers final: 22 residues processed: 174 average time/residue: 0.3153 time to fit residues: 88.1529 Evaluate side-chains 170 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1024 THR Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.1980 chunk 236 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 218 optimal weight: 0.0070 chunk 121 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21648 Z= 0.158 Angle : 0.622 12.770 29348 Z= 0.308 Chirality : 0.042 0.153 3276 Planarity : 0.004 0.045 3848 Dihedral : 5.010 56.267 3042 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.37 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.50 (0.16), residues: 2740 helix: 1.10 (0.15), residues: 1216 sheet: -0.62 (0.26), residues: 388 loop : -0.01 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 838 HIS 0.004 0.001 HIS A1059 PHE 0.019 0.001 PHE E1078 TYR 0.017 0.001 TYR B 722 ARG 0.006 0.000 ARG E 818 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 881 MET cc_start: 0.7952 (mmt) cc_final: 0.7652 (mmp) REVERT: A 1087 ILE cc_start: 0.4880 (OUTLIER) cc_final: 0.4636 (tp) REVERT: A 1116 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.3519 (ptp) REVERT: B 616 MET cc_start: 0.8287 (mmm) cc_final: 0.7925 (mmm) REVERT: B 641 MET cc_start: 0.6512 (ptt) cc_final: 0.5924 (ptt) REVERT: B 686 MET cc_start: 0.9083 (mpp) cc_final: 0.8803 (mpp) REVERT: C 641 MET cc_start: 0.7996 (ppp) cc_final: 0.7356 (ppp) REVERT: C 743 MET cc_start: 0.5013 (tpt) cc_final: 0.4460 (tpt) REVERT: C 900 MET cc_start: 0.7287 (ttp) cc_final: 0.6862 (ttm) REVERT: C 921 MET cc_start: 0.6939 (mpp) cc_final: 0.6707 (mpp) REVERT: C 1116 MET cc_start: 0.7057 (pmm) cc_final: 0.6766 (pmm) REVERT: E 604 MET cc_start: 0.7120 (ppp) cc_final: 0.6558 (ppp) REVERT: E 921 MET cc_start: 0.7316 (mmm) cc_final: 0.6919 (mmm) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.3021 time to fit residues: 87.1782 Evaluate side-chains 172 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1169 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.0370 chunk 29 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN E 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21648 Z= 0.167 Angle : 0.626 13.325 29348 Z= 0.307 Chirality : 0.042 0.172 3276 Planarity : 0.004 0.047 3848 Dihedral : 4.730 54.544 3039 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.55 % Allowed : 12.63 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.59 (0.16), residues: 2740 helix: 1.19 (0.15), residues: 1220 sheet: -0.63 (0.26), residues: 392 loop : 0.05 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 838 HIS 0.004 0.001 HIS A1101 PHE 0.018 0.001 PHE E1078 TYR 0.014 0.001 TYR C 722 ARG 0.006 0.000 ARG E 818 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1087 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4928 (tp) REVERT: A 1116 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.3506 (ptp) REVERT: B 616 MET cc_start: 0.8417 (mmm) cc_final: 0.8075 (mmm) REVERT: B 641 MET cc_start: 0.6650 (ptt) cc_final: 0.6040 (ptt) REVERT: C 743 MET cc_start: 0.4989 (tpt) cc_final: 0.4436 (tpt) REVERT: C 854 MET cc_start: 0.6556 (ppp) cc_final: 0.6347 (ppp) REVERT: C 900 MET cc_start: 0.7209 (ttp) cc_final: 0.6903 (ttm) REVERT: C 1116 MET cc_start: 0.7105 (pmm) cc_final: 0.6826 (pmm) REVERT: E 566 MET cc_start: 0.4692 (tpt) cc_final: 0.4425 (tpt) REVERT: E 671 MET cc_start: 0.4411 (tpp) cc_final: 0.4035 (tpp) REVERT: E 921 MET cc_start: 0.7484 (mmm) cc_final: 0.7194 (mmm) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 0.2969 time to fit residues: 85.3633 Evaluate side-chains 171 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1169 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21648 Z= 0.200 Angle : 0.659 13.217 29348 Z= 0.328 Chirality : 0.043 0.271 3276 Planarity : 0.005 0.041 3848 Dihedral : 4.758 53.713 3035 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 13.03 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.47 (0.16), residues: 2740 helix: 1.07 (0.15), residues: 1220 sheet: -0.68 (0.26), residues: 392 loop : -0.01 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 838 HIS 0.005 0.001 HIS B1099 PHE 0.017 0.002 PHE C1078 TYR 0.014 0.001 TYR C 722 ARG 0.015 0.001 ARG E1074 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 MET cc_start: 0.5621 (tpt) cc_final: 0.5322 (tpt) REVERT: B 641 MET cc_start: 0.6640 (ptt) cc_final: 0.6147 (ptt) REVERT: C 641 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7695 (ppp) REVERT: C 743 MET cc_start: 0.5238 (tpt) cc_final: 0.4580 (tpt) REVERT: C 1116 MET cc_start: 0.7138 (pmm) cc_final: 0.6850 (pmm) REVERT: E 566 MET cc_start: 0.5099 (tpt) cc_final: 0.4633 (tpt) REVERT: E 671 MET cc_start: 0.4813 (tpp) cc_final: 0.4528 (tpp) REVERT: E 921 MET cc_start: 0.7626 (mmm) cc_final: 0.7401 (mmm) outliers start: 32 outliers final: 23 residues processed: 172 average time/residue: 0.3092 time to fit residues: 85.5197 Evaluate side-chains 167 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21648 Z= 0.266 Angle : 0.741 13.447 29348 Z= 0.374 Chirality : 0.045 0.237 3276 Planarity : 0.005 0.045 3848 Dihedral : 5.199 54.937 3035 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.28 % Allowed : 13.30 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.01 (0.16), residues: 2740 helix: 0.60 (0.15), residues: 1220 sheet: -0.84 (0.26), residues: 392 loop : -0.19 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 607 HIS 0.009 0.001 HIS A1101 PHE 0.030 0.002 PHE C1078 TYR 0.014 0.002 TYR E 722 ARG 0.013 0.001 ARG C1085 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.7369 (mmm) cc_final: 0.7034 (mmm) REVERT: B 566 MET cc_start: 0.4109 (OUTLIER) cc_final: 0.3037 (mmp) REVERT: B 743 MET cc_start: 0.6196 (tpt) cc_final: 0.5971 (tpt) REVERT: C 604 MET cc_start: 0.5592 (mmm) cc_final: 0.5364 (mmp) REVERT: C 1116 MET cc_start: 0.7536 (pmm) cc_final: 0.7286 (pmm) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 0.3238 time to fit residues: 88.4946 Evaluate side-chains 160 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1087 ILE Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.9160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21648 Z= 0.265 Angle : 0.760 18.280 29348 Z= 0.380 Chirality : 0.045 0.277 3276 Planarity : 0.005 0.052 3848 Dihedral : 5.253 54.675 3035 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.06 % Allowed : 13.96 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.14 (0.16), residues: 2740 helix: 0.47 (0.14), residues: 1216 sheet: -0.78 (0.26), residues: 384 loop : -0.27 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 607 HIS 0.005 0.001 HIS A1059 PHE 0.028 0.002 PHE A 763 TYR 0.015 0.002 TYR C 722 ARG 0.010 0.001 ARG C1085 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 MET cc_start: 0.7536 (mmm) cc_final: 0.7336 (mmm) REVERT: A 804 MET cc_start: 0.8272 (mmp) cc_final: 0.8043 (mmp) REVERT: A 1098 MET cc_start: 0.5389 (tpt) cc_final: 0.4989 (tpt) REVERT: B 566 MET cc_start: 0.3968 (OUTLIER) cc_final: 0.2860 (mmp) REVERT: B 641 MET cc_start: 0.6700 (ptt) cc_final: 0.5920 (ptt) REVERT: B 743 MET cc_start: 0.6263 (tpt) cc_final: 0.6006 (tpt) REVERT: C 641 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7936 (ppp) REVERT: C 743 MET cc_start: 0.5997 (tpt) cc_final: 0.5016 (tpt) REVERT: C 1116 MET cc_start: 0.7512 (pmm) cc_final: 0.7303 (pmm) REVERT: E 566 MET cc_start: 0.5062 (tpt) cc_final: 0.4769 (tpt) REVERT: E 671 MET cc_start: 0.5782 (tpp) cc_final: 0.5259 (tpp) outliers start: 24 outliers final: 20 residues processed: 162 average time/residue: 0.2711 time to fit residues: 70.7995 Evaluate side-chains 160 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1087 ILE Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 221 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.0070 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 771 HIS E 807 GLN E1075 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.053123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.045080 restraints weight = 205652.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.046105 restraints weight = 129209.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.046751 restraints weight = 90106.193| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.9136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21648 Z= 0.162 Angle : 0.737 19.838 29348 Z= 0.357 Chirality : 0.044 0.208 3276 Planarity : 0.004 0.046 3848 Dihedral : 4.907 53.566 3035 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.97 % Allowed : 13.96 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.35 (0.17), residues: 2740 helix: 0.93 (0.15), residues: 1220 sheet: -0.42 (0.28), residues: 352 loop : -0.16 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 607 HIS 0.003 0.001 HIS B 769 PHE 0.026 0.002 PHE A 763 TYR 0.016 0.001 TYR C 722 ARG 0.018 0.001 ARG C 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.30 seconds wall clock time: 68 minutes 23.31 seconds (4103.31 seconds total)