Starting phenix.real_space_refine on Sun Oct 12 05:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_36044_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_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/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_36044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_36044.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_36044_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7o_36044/10_2025/8j7o_36044_neut_trim.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.27, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 959.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.98 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: 4.10 Time building geometry restraints manager: 2.50 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: 0.02 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- 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 : 0.013 0.373 21652 Z= 0.877 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.001 ARG A 732 TYR 0.097 0.016 TYR E 593 PHE 0.053 0.010 PHE A 618 TRP 0.022 0.005 TRP B 624 HIS 0.029 0.004 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.01202 (21648) covalent geometry : angle 1.60271 (29348) hydrogen bonds : bond 0.18320 ( 995) hydrogen bonds : angle 7.83109 ( 2808) Misc. bond : bond 0.37284 ( 4) *********************** 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 to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.716 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: symmetry clash REVERT: B 634 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6726 (mp) REVERT: E 606 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6147 (p0) REVERT: E 783 MET cc_start: 0.7424 (mmp) cc_final: 0.7221 (mmp) REVERT: E 1166 MET cc_start: 0.2997 (ttt) cc_final: 0.2596 (mtp) outliers start: 60 outliers final: 14 residues processed: 400 average time/residue: 0.1911 time to fit residues: 110.9208 Evaluate side-chains 196 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET 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 566 MET 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 898 ASN 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 C 898 ASN C1019 HIS C1075 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN E1075 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.062581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.053533 restraints weight = 197946.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.054787 restraints weight = 132139.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.055701 restraints weight = 95547.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.056238 restraints weight = 74240.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.056634 restraints weight = 62197.288| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21652 Z= 0.206 Angle : 0.727 13.136 29348 Z= 0.374 Chirality : 0.045 0.203 3276 Planarity : 0.005 0.061 3848 Dihedral : 6.970 69.230 3083 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.21 % Allowed : 9.63 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 2740 helix: 1.31 (0.15), residues: 1216 sheet: -0.30 (0.27), residues: 368 loop : 0.28 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 977 TYR 0.023 0.002 TYR E 503 PHE 0.031 0.002 PHE A1078 TRP 0.026 0.003 TRP A 838 HIS 0.008 0.002 HIS C1019 Details of bonding type rmsd covalent geometry : bond 0.00423 (21648) covalent geometry : angle 0.72679 (29348) hydrogen bonds : bond 0.04675 ( 995) hydrogen bonds : angle 5.73520 ( 2808) Misc. bond : bond 0.00652 ( 4) *********************** 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 232 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.815 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: A 686 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8921 (mpp) REVERT: A 804 MET cc_start: 0.8989 (mmp) cc_final: 0.8403 (mmp) REVERT: A 921 MET cc_start: 0.7872 (mmm) cc_final: 0.7182 (mmm) REVERT: A 986 ASP cc_start: 0.7807 (t0) cc_final: 0.7547 (t0) REVERT: B 607 TRP cc_start: 0.6098 (OUTLIER) cc_final: 0.5163 (t60) REVERT: B 641 MET cc_start: 0.7590 (ptm) cc_final: 0.6807 (ptm) REVERT: B 804 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7436 (mmp) REVERT: B 810 MET cc_start: 0.5828 (tmm) cc_final: 0.5537 (tmm) REVERT: B 854 MET cc_start: 0.6381 (tmm) cc_final: 0.5477 (ppp) REVERT: B 1058 LEU cc_start: 0.9523 (tp) cc_final: 0.9251 (tp) REVERT: C 500 LEU cc_start: 0.9432 (mt) cc_final: 0.9190 (mt) REVERT: C 571 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: C 743 MET cc_start: 0.4806 (tpt) cc_final: 0.4417 (tpt) REVERT: C 756 VAL cc_start: 0.8237 (t) cc_final: 0.8032 (t) REVERT: C 854 MET cc_start: 0.6911 (ppp) cc_final: 0.6287 (ppp) REVERT: E 641 MET cc_start: 0.6197 (ptm) cc_final: 0.5754 (ptm) REVERT: E 1166 MET cc_start: 0.2641 (ttt) cc_final: 0.2418 (mtp) outliers start: 50 outliers final: 22 residues processed: 219 average time/residue: 0.1601 time to fit residues: 55.0353 Evaluate side-chains 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 VAL 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 784 LEU Chi-restraints excluded: chain B residue 804 MET 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 631 ARG 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 545 LEU Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 658 VAL 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 121 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 179 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 B1135 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 ASN E 807 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.061808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.052712 restraints weight = 198245.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.053946 restraints weight = 131280.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.054853 restraints weight = 94118.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.055438 restraints weight = 72922.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.055822 restraints weight = 60402.988| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21652 Z= 0.127 Angle : 0.606 13.918 29348 Z= 0.306 Chirality : 0.043 0.158 3276 Planarity : 0.005 0.042 3848 Dihedral : 5.719 59.818 3061 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.59 % Allowed : 10.47 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2740 helix: 1.51 (0.15), residues: 1220 sheet: -0.45 (0.26), residues: 392 loop : 0.39 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 542 TYR 0.017 0.001 TYR C 722 PHE 0.023 0.002 PHE C1078 TRP 0.028 0.003 TRP E 607 HIS 0.003 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00263 (21648) covalent geometry : angle 0.60630 (29348) hydrogen bonds : bond 0.04225 ( 995) hydrogen bonds : angle 5.25406 ( 2808) Misc. bond : bond 0.00030 ( 4) *********************** 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 198 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.827 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: A 686 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8848 (mpp) REVERT: A 804 MET cc_start: 0.9056 (mmp) cc_final: 0.8495 (mmp) REVERT: A 921 MET cc_start: 0.7807 (mmm) cc_final: 0.7180 (mmm) REVERT: A 986 ASP cc_start: 0.7776 (t0) cc_final: 0.7521 (t0) REVERT: B 607 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.6068 (t60) REVERT: B 641 MET cc_start: 0.7356 (ptm) cc_final: 0.6963 (ptt) REVERT: B 686 MET cc_start: 0.9280 (ptp) cc_final: 0.8890 (mpp) REVERT: B 900 MET cc_start: 0.6601 (ttp) cc_final: 0.6381 (ttp) REVERT: B 1100 PHE cc_start: 0.4798 (m-10) cc_final: 0.3327 (m-10) REVERT: C 496 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6163 (mmm160) REVERT: C 500 LEU cc_start: 0.9445 (mt) cc_final: 0.9199 (mt) REVERT: C 571 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7530 (ttp80) REVERT: C 743 MET cc_start: 0.4660 (tpt) cc_final: 0.4252 (tpt) REVERT: C 804 MET cc_start: 0.8001 (mmp) cc_final: 0.7557 (mmp) REVERT: C 854 MET cc_start: 0.7012 (ppp) cc_final: 0.6365 (ppp) REVERT: C 921 MET cc_start: 0.7485 (mmm) cc_final: 0.7088 (mmm) REVERT: E 508 MET cc_start: 0.8820 (mmm) cc_final: 0.8508 (tpp) REVERT: E 641 MET cc_start: 0.6246 (ptm) cc_final: 0.6036 (ptm) REVERT: E 690 MET cc_start: 0.8951 (tmm) cc_final: 0.8691 (tmm) REVERT: E 1166 MET cc_start: 0.2711 (ttt) cc_final: 0.2464 (mtp) outliers start: 36 outliers final: 18 residues processed: 189 average time/residue: 0.1615 time to fit residues: 47.8655 Evaluate side-chains 175 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 571 ARG Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1044 ILE 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 1000 GLU Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 182 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 198 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 502 HIS ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS B1135 GLN C 502 HIS C 560 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.058032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.049231 restraints weight = 203925.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.050373 restraints weight = 133804.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.051191 restraints weight = 96044.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.051664 restraints weight = 74929.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.052061 restraints weight = 63267.691| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21652 Z= 0.183 Angle : 0.659 15.849 29348 Z= 0.337 Chirality : 0.043 0.162 3276 Planarity : 0.005 0.047 3848 Dihedral : 5.356 56.556 3053 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.99 % Allowed : 10.56 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2740 helix: 1.19 (0.15), residues: 1220 sheet: -0.38 (0.26), residues: 388 loop : 0.11 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1036 TYR 0.015 0.002 TYR C 722 PHE 0.028 0.002 PHE E1100 TRP 0.026 0.003 TRP E 607 HIS 0.005 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00389 (21648) covalent geometry : angle 0.65914 (29348) hydrogen bonds : bond 0.04204 ( 995) hydrogen bonds : angle 5.28658 ( 2808) Misc. bond : bond 0.00010 ( 4) *********************** 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 204 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.867 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 639 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: A 686 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (mpp) REVERT: A 804 MET cc_start: 0.9188 (mmp) cc_final: 0.8558 (mmp) REVERT: A 986 ASP cc_start: 0.7509 (t0) cc_final: 0.7219 (t0) REVERT: A 1116 MET cc_start: 0.3108 (OUTLIER) cc_final: 0.2848 (ptp) REVERT: B 616 MET cc_start: 0.8867 (mmm) cc_final: 0.8586 (mmm) REVERT: B 900 MET cc_start: 0.7085 (ttp) cc_final: 0.6787 (ttp) REVERT: B 921 MET cc_start: 0.8739 (mmm) cc_final: 0.8410 (mmm) REVERT: B 1100 PHE cc_start: 0.4165 (m-10) cc_final: 0.3508 (m-10) REVERT: C 496 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7113 (mmm160) REVERT: C 571 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: C 641 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6207 (ppp) REVERT: C 671 MET cc_start: 0.7762 (tpp) cc_final: 0.7504 (tpp) REVERT: C 743 MET cc_start: 0.5067 (tpt) cc_final: 0.4540 (tpt) REVERT: C 854 MET cc_start: 0.7194 (ppp) cc_final: 0.6721 (ppp) REVERT: C 921 MET cc_start: 0.7790 (mmm) cc_final: 0.7579 (mmm) REVERT: C 1166 MET cc_start: 0.2811 (ttt) cc_final: 0.2388 (ptm) REVERT: E 508 MET cc_start: 0.8885 (mmm) cc_final: 0.8627 (tpp) REVERT: E 641 MET cc_start: 0.6782 (ptm) cc_final: 0.6182 (ptm) REVERT: E 1053 GLU cc_start: 0.5807 (mt-10) cc_final: 0.5549 (pt0) REVERT: E 1166 MET cc_start: 0.2570 (ttt) cc_final: 0.2282 (mtp) outliers start: 45 outliers final: 17 residues processed: 192 average time/residue: 0.1458 time to fit residues: 45.1983 Evaluate side-chains 173 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 639 PHE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 766 LEU 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 A residue 1145 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 828 MET 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 641 MET 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 1096 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 202 optimal weight: 10.0000 chunk 248 optimal weight: 0.0000 chunk 66 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- 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 875 HIS ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 875 HIS E1073 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.056631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.047932 restraints weight = 204393.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.049047 restraints weight = 133756.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.049806 restraints weight = 95927.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.050297 restraints weight = 74946.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.050677 restraints weight = 63028.315| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21652 Z= 0.166 Angle : 0.620 14.309 29348 Z= 0.318 Chirality : 0.043 0.168 3276 Planarity : 0.005 0.040 3848 Dihedral : 5.105 57.738 3047 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.08 % Allowed : 11.40 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.16), residues: 2740 helix: 1.12 (0.15), residues: 1216 sheet: -0.49 (0.27), residues: 372 loop : -0.00 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 818 TYR 0.016 0.002 TYR C 722 PHE 0.024 0.002 PHE E1078 TRP 0.024 0.002 TRP B 607 HIS 0.006 0.001 HIS C 506 Details of bonding type rmsd covalent geometry : bond 0.00331 (21648) covalent geometry : angle 0.62002 (29348) hydrogen bonds : bond 0.04046 ( 995) hydrogen bonds : angle 5.19621 ( 2808) Misc. bond : bond 0.00020 ( 4) *********************** 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 200 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.911 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: A 639 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6504 (m-10) REVERT: A 804 MET cc_start: 0.9221 (mmp) cc_final: 0.8722 (mmp) REVERT: A 921 MET cc_start: 0.8208 (mmm) cc_final: 0.7579 (mmm) REVERT: A 986 ASP cc_start: 0.7405 (t0) cc_final: 0.7119 (t0) REVERT: A 1087 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5133 (pt) REVERT: A 1116 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.2895 (ptp) REVERT: B 616 MET cc_start: 0.9022 (mmm) cc_final: 0.8738 (mmm) REVERT: B 641 MET cc_start: 0.7190 (ptm) cc_final: 0.6895 (ptt) REVERT: B 686 MET cc_start: 0.9386 (ptp) cc_final: 0.9159 (mpp) REVERT: B 743 MET cc_start: 0.6069 (tpt) cc_final: 0.5745 (tpt) REVERT: B 804 MET cc_start: 0.6706 (mmp) cc_final: 0.6265 (mmp) REVERT: B 921 MET cc_start: 0.8825 (mmm) cc_final: 0.8610 (mmm) REVERT: B 986 ASP cc_start: 0.8319 (t0) cc_final: 0.8089 (t0) REVERT: B 1076 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 496 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7926 (mmm160) REVERT: C 671 MET cc_start: 0.7874 (tpp) cc_final: 0.7553 (tpp) REVERT: C 743 MET cc_start: 0.5423 (tpt) cc_final: 0.4717 (tpt) REVERT: C 804 MET cc_start: 0.8010 (mmp) cc_final: 0.7511 (mmp) REVERT: C 921 MET cc_start: 0.7919 (mmm) cc_final: 0.7577 (mmm) REVERT: C 1153 MET cc_start: 0.5201 (tmm) cc_final: 0.4857 (tmm) REVERT: E 724 MET cc_start: 0.8386 (ptp) cc_final: 0.7973 (mmt) REVERT: E 783 MET cc_start: 0.6788 (tpp) cc_final: 0.6585 (tpp) REVERT: E 921 MET cc_start: 0.8365 (mmm) cc_final: 0.7899 (mmm) REVERT: E 1098 MET cc_start: 0.7324 (tpt) cc_final: 0.7005 (tpt) REVERT: E 1166 MET cc_start: 0.2663 (ttt) cc_final: 0.2423 (mtp) outliers start: 47 outliers final: 26 residues processed: 183 average time/residue: 0.1462 time to fit residues: 42.9579 Evaluate side-chains 178 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 566 MET Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 639 PHE 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 A residue 1145 MET Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1101 HIS 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 631 ARG 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 C residue 1126 VAL 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 1096 LYS 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: 0.8980 chunk 131 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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** E 640 GLN ** E1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.055920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.047355 restraints weight = 204523.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.048414 restraints weight = 133884.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.049108 restraints weight = 94959.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.049669 restraints weight = 75867.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.049997 restraints weight = 62770.805| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21652 Z= 0.138 Angle : 0.612 13.904 29348 Z= 0.308 Chirality : 0.042 0.155 3276 Planarity : 0.005 0.041 3848 Dihedral : 4.952 55.515 3047 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.81 % Allowed : 12.32 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2740 helix: 1.28 (0.15), residues: 1220 sheet: -0.55 (0.26), residues: 392 loop : 0.05 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 818 TYR 0.015 0.002 TYR C 722 PHE 0.021 0.002 PHE E1078 TRP 0.016 0.002 TRP E 607 HIS 0.005 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00288 (21648) covalent geometry : angle 0.61158 (29348) hydrogen bonds : bond 0.03806 ( 995) hydrogen bonds : angle 5.14495 ( 2808) Misc. bond : bond 0.00010 ( 4) *********************** 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 197 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.899 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 604 MET cc_start: 0.8176 (pmm) cc_final: 0.7765 (pmm) REVERT: A 616 MET cc_start: 0.7390 (mmm) cc_final: 0.6655 (mmm) REVERT: A 639 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: A 671 MET cc_start: 0.6694 (tpp) cc_final: 0.6359 (tpp) REVERT: A 804 MET cc_start: 0.9204 (mmp) cc_final: 0.8697 (mmp) REVERT: A 881 MET cc_start: 0.8746 (mmt) cc_final: 0.8495 (mmm) REVERT: A 921 MET cc_start: 0.8399 (mmm) cc_final: 0.8192 (mmm) REVERT: A 986 ASP cc_start: 0.7470 (t0) cc_final: 0.7216 (t0) REVERT: A 1087 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.5718 (pt) REVERT: A 1095 MET cc_start: 0.6963 (pmm) cc_final: 0.6613 (pmm) REVERT: A 1116 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3160 (ptp) REVERT: B 566 MET cc_start: 0.6019 (ttp) cc_final: 0.5799 (ttp) REVERT: B 604 MET cc_start: 0.7824 (ptm) cc_final: 0.7442 (ptm) REVERT: B 616 MET cc_start: 0.9000 (mmm) cc_final: 0.8755 (mmm) REVERT: B 641 MET cc_start: 0.7151 (ptm) cc_final: 0.6596 (ptt) REVERT: B 686 MET cc_start: 0.9447 (ptp) cc_final: 0.9186 (mpp) REVERT: B 743 MET cc_start: 0.6082 (tpt) cc_final: 0.5766 (tpt) REVERT: B 804 MET cc_start: 0.7258 (mmp) cc_final: 0.6872 (mmp) REVERT: B 921 MET cc_start: 0.9057 (mmm) cc_final: 0.8725 (mmm) REVERT: B 1076 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 496 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8137 (mmm160) REVERT: C 641 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6200 (ppp) REVERT: C 671 MET cc_start: 0.7724 (tpp) cc_final: 0.7438 (tpp) REVERT: C 743 MET cc_start: 0.5406 (tpt) cc_final: 0.4832 (tpt) REVERT: C 804 MET cc_start: 0.7942 (mmp) cc_final: 0.7630 (mmp) REVERT: C 1166 MET cc_start: 0.2803 (ttt) cc_final: 0.2368 (ptm) REVERT: E 500 LEU cc_start: 0.9103 (mt) cc_final: 0.8857 (mt) REVERT: E 508 MET cc_start: 0.8945 (tpp) cc_final: 0.8506 (tpp) REVERT: E 641 MET cc_start: 0.6172 (ptm) cc_final: 0.5782 (ppp) REVERT: E 724 MET cc_start: 0.8527 (ptp) cc_final: 0.8250 (mmt) outliers start: 41 outliers final: 20 residues processed: 183 average time/residue: 0.1447 time to fit residues: 42.6041 Evaluate side-chains 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 639 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS 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 641 MET Chi-restraints excluded: chain C residue 653 ASN 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 905 ILE Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1096 LYS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 27 optimal weight: 0.0980 chunk 52 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN C 875 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 ASN E 807 GLN ** E1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.052851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.044791 restraints weight = 212652.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.045830 restraints weight = 136967.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.046551 restraints weight = 96681.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.046979 restraints weight = 75035.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.047296 restraints weight = 63050.148| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21652 Z= 0.209 Angle : 0.737 15.836 29348 Z= 0.375 Chirality : 0.045 0.202 3276 Planarity : 0.005 0.057 3848 Dihedral : 5.355 56.622 3047 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.03 % Allowed : 12.23 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.16), residues: 2740 helix: 0.70 (0.14), residues: 1220 sheet: -0.72 (0.28), residues: 344 loop : -0.24 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.023 0.002 TYR B 722 PHE 0.021 0.002 PHE C1078 TRP 0.020 0.002 TRP E 607 HIS 0.009 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00423 (21648) covalent geometry : angle 0.73689 (29348) hydrogen bonds : bond 0.04417 ( 995) hydrogen bonds : angle 5.43969 ( 2808) Misc. bond : bond 0.00028 ( 4) *********************** 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 203 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.965 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: A 616 MET cc_start: 0.7561 (mmm) cc_final: 0.6907 (mmm) REVERT: A 639 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6815 (m-10) REVERT: A 671 MET cc_start: 0.6860 (tpp) cc_final: 0.6579 (tpp) REVERT: A 804 MET cc_start: 0.9160 (mmp) cc_final: 0.8957 (mmp) REVERT: A 986 ASP cc_start: 0.7429 (t0) cc_final: 0.7179 (t0) REVERT: A 1087 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.6831 (pt) REVERT: A 1095 MET cc_start: 0.7038 (pmm) cc_final: 0.6808 (pmm) REVERT: B 604 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7619 (ptm) REVERT: B 616 MET cc_start: 0.9006 (mmm) cc_final: 0.8775 (mmm) REVERT: B 641 MET cc_start: 0.7371 (ptm) cc_final: 0.7114 (ptt) REVERT: B 686 MET cc_start: 0.9439 (ptp) cc_final: 0.9234 (mpp) REVERT: B 743 MET cc_start: 0.6332 (tpt) cc_final: 0.5856 (tpt) REVERT: B 804 MET cc_start: 0.7294 (mmp) cc_final: 0.7057 (mmp) REVERT: B 921 MET cc_start: 0.9123 (mmm) cc_final: 0.8903 (mmm) REVERT: B 1076 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 641 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6407 (ppp) REVERT: C 671 MET cc_start: 0.7661 (tpp) cc_final: 0.7252 (tpp) REVERT: C 804 MET cc_start: 0.8249 (mmp) cc_final: 0.7958 (mmp) REVERT: C 1166 MET cc_start: 0.3049 (ttt) cc_final: 0.2533 (ptm) REVERT: E 500 LEU cc_start: 0.9220 (mt) cc_final: 0.9000 (mt) REVERT: E 641 MET cc_start: 0.7337 (ptm) cc_final: 0.6953 (ptm) REVERT: E 724 MET cc_start: 0.8743 (ptp) cc_final: 0.8409 (mmt) REVERT: E 784 LEU cc_start: 0.8846 (pp) cc_final: 0.8304 (mm) REVERT: E 801 MET cc_start: 0.8633 (mmm) cc_final: 0.8350 (mmm) REVERT: E 854 MET cc_start: 0.7082 (tpt) cc_final: 0.6829 (tpt) REVERT: E 921 MET cc_start: 0.8192 (mmm) cc_final: 0.7854 (mmm) outliers start: 46 outliers final: 27 residues processed: 191 average time/residue: 0.1445 time to fit residues: 44.8279 Evaluate side-chains 182 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 639 PHE Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 987 LEU 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 1153 MET Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 500 LEU 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 1065 VAL 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 997 ARG Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1096 LYS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 681 ASN ** E1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.054430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.046041 restraints weight = 208278.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.047105 restraints weight = 134016.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.047857 restraints weight = 95030.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.048303 restraints weight = 73825.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.048628 restraints weight = 62055.822| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21652 Z= 0.111 Angle : 0.635 13.305 29348 Z= 0.316 Chirality : 0.043 0.175 3276 Planarity : 0.004 0.046 3848 Dihedral : 4.836 55.313 3039 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.10 % Allowed : 13.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2740 helix: 1.15 (0.15), residues: 1220 sheet: -0.58 (0.28), residues: 344 loop : -0.09 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 542 TYR 0.017 0.001 TYR C 722 PHE 0.029 0.002 PHE A 763 TRP 0.031 0.002 TRP E 607 HIS 0.003 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00229 (21648) covalent geometry : angle 0.63479 (29348) hydrogen bonds : bond 0.03762 ( 995) hydrogen bonds : angle 5.15782 ( 2808) Misc. bond : bond 0.00011 ( 4) *********************** 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 180 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.915 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: A 616 MET cc_start: 0.7545 (mmm) cc_final: 0.6901 (mmm) REVERT: A 639 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: A 671 MET cc_start: 0.6747 (tpp) cc_final: 0.6200 (tpp) REVERT: A 804 MET cc_start: 0.9187 (mmp) cc_final: 0.8841 (mmp) REVERT: A 986 ASP cc_start: 0.7493 (t0) cc_final: 0.7242 (t0) REVERT: A 1087 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.6589 (pt) REVERT: A 1095 MET cc_start: 0.6973 (pmm) cc_final: 0.6765 (pmm) REVERT: B 604 MET cc_start: 0.7993 (ptm) cc_final: 0.7700 (ptm) REVERT: B 616 MET cc_start: 0.8970 (mmm) cc_final: 0.8687 (mmm) REVERT: B 641 MET cc_start: 0.7080 (ptm) cc_final: 0.6598 (ptt) REVERT: B 743 MET cc_start: 0.6315 (tpt) cc_final: 0.6004 (tpt) REVERT: B 754 MET cc_start: 0.8738 (ttp) cc_final: 0.8478 (ptp) REVERT: B 804 MET cc_start: 0.7288 (mmp) cc_final: 0.7065 (mmp) REVERT: B 921 MET cc_start: 0.9069 (mmm) cc_final: 0.8855 (mmm) REVERT: B 1076 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8902 (p) REVERT: C 641 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6194 (ppp) REVERT: C 671 MET cc_start: 0.7503 (tpp) cc_final: 0.7063 (tpp) REVERT: C 743 MET cc_start: 0.5988 (tpt) cc_final: 0.5251 (tpt) REVERT: C 804 MET cc_start: 0.8136 (mmp) cc_final: 0.7655 (mmp) REVERT: C 921 MET cc_start: 0.8321 (mmm) cc_final: 0.7404 (mpp) REVERT: C 1166 MET cc_start: 0.3170 (ttt) cc_final: 0.2696 (ptm) REVERT: E 500 LEU cc_start: 0.9216 (mt) cc_final: 0.8995 (mt) REVERT: E 605 GLU cc_start: 0.2662 (OUTLIER) cc_final: 0.2298 (tp30) REVERT: E 641 MET cc_start: 0.6652 (ptm) cc_final: 0.6362 (ppp) REVERT: E 724 MET cc_start: 0.8624 (ptp) cc_final: 0.8228 (mmt) REVERT: E 784 LEU cc_start: 0.8710 (pp) cc_final: 0.8191 (mm) REVERT: E 801 MET cc_start: 0.8636 (mmm) cc_final: 0.8396 (mmm) REVERT: E 854 MET cc_start: 0.7085 (tpt) cc_final: 0.6854 (tpt) REVERT: E 921 MET cc_start: 0.8455 (mmm) cc_final: 0.8195 (mmm) REVERT: E 1051 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 25 outliers final: 13 residues processed: 176 average time/residue: 0.1460 time to fit residues: 42.1040 Evaluate side-chains 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 639 PHE 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 1153 MET Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 681 ASN Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 213 optimal weight: 7.9990 chunk 266 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 ASN ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1073 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.054304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.045955 restraints weight = 208198.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.047005 restraints weight = 134019.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.047760 restraints weight = 94463.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.048214 restraints weight = 73168.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.048532 restraints weight = 61399.343| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.8041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21652 Z= 0.109 Angle : 0.635 13.553 29348 Z= 0.317 Chirality : 0.043 0.189 3276 Planarity : 0.005 0.152 3848 Dihedral : 4.537 47.166 3036 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.06 % Allowed : 13.56 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2740 helix: 1.13 (0.15), residues: 1240 sheet: -0.47 (0.28), residues: 344 loop : -0.11 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1085 TYR 0.013 0.001 TYR B 722 PHE 0.024 0.001 PHE A 763 TRP 0.017 0.002 TRP E 607 HIS 0.003 0.001 HIS E 773 Details of bonding type rmsd covalent geometry : bond 0.00228 (21648) covalent geometry : angle 0.63537 (29348) hydrogen bonds : bond 0.03645 ( 995) hydrogen bonds : angle 5.14421 ( 2808) Misc. bond : bond 0.00017 ( 4) *********************** 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 173 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.788 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: A 616 MET cc_start: 0.7631 (mmm) cc_final: 0.6943 (mmm) REVERT: A 639 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7118 (m-10) REVERT: A 671 MET cc_start: 0.6827 (tpp) cc_final: 0.6215 (tpp) REVERT: A 743 MET cc_start: 0.6343 (tpt) cc_final: 0.5846 (tpt) REVERT: A 804 MET cc_start: 0.9197 (mmp) cc_final: 0.8825 (mmp) REVERT: A 921 MET cc_start: 0.8369 (mmm) cc_final: 0.7871 (mmm) REVERT: A 986 ASP cc_start: 0.7467 (t0) cc_final: 0.7201 (t0) REVERT: A 1087 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.6675 (pt) REVERT: A 1095 MET cc_start: 0.6998 (pmm) cc_final: 0.6796 (pmm) REVERT: B 604 MET cc_start: 0.7851 (ptm) cc_final: 0.7610 (ptm) REVERT: B 616 MET cc_start: 0.9006 (mmm) cc_final: 0.8740 (mmm) REVERT: B 641 MET cc_start: 0.7048 (ptm) cc_final: 0.6538 (ptt) REVERT: B 743 MET cc_start: 0.6317 (tpt) cc_final: 0.6057 (tpt) REVERT: B 804 MET cc_start: 0.7238 (mmp) cc_final: 0.7000 (mmp) REVERT: B 921 MET cc_start: 0.9091 (mmm) cc_final: 0.8880 (mmm) REVERT: B 1076 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8899 (p) REVERT: C 641 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6275 (ppp) REVERT: C 671 MET cc_start: 0.7557 (tpp) cc_final: 0.7060 (tpp) REVERT: C 743 MET cc_start: 0.6085 (tpt) cc_final: 0.5410 (tpt) REVERT: C 804 MET cc_start: 0.8119 (mmp) cc_final: 0.7729 (mmp) REVERT: C 1166 MET cc_start: 0.3129 (ttt) cc_final: 0.2657 (ptm) REVERT: E 546 LEU cc_start: 0.8862 (tt) cc_final: 0.8577 (mp) REVERT: E 724 MET cc_start: 0.8659 (ptp) cc_final: 0.8232 (mmt) REVERT: E 743 MET cc_start: 0.5939 (tpt) cc_final: 0.5145 (mmm) REVERT: E 783 MET cc_start: 0.7247 (tpp) cc_final: 0.7021 (tpp) REVERT: E 784 LEU cc_start: 0.8807 (pp) cc_final: 0.8333 (mm) REVERT: E 801 MET cc_start: 0.8648 (mmm) cc_final: 0.8432 (mmm) REVERT: E 854 MET cc_start: 0.6990 (tpt) cc_final: 0.6735 (tpt) REVERT: E 921 MET cc_start: 0.8468 (mmm) cc_final: 0.8230 (mmm) REVERT: E 1051 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 24 outliers final: 17 residues processed: 167 average time/residue: 0.1373 time to fit residues: 38.2820 Evaluate side-chains 170 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 639 PHE 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 1153 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1076 VAL 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 653 ASN Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1096 LYS Chi-restraints excluded: chain E residue 1169 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 228 optimal weight: 0.0980 chunk 162 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.054000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.045715 restraints weight = 209486.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.046796 restraints weight = 134573.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.047448 restraints weight = 94835.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.047943 restraints weight = 74714.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.048241 restraints weight = 62250.596| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.8247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21652 Z= 0.112 Angle : 0.654 20.893 29348 Z= 0.325 Chirality : 0.043 0.269 3276 Planarity : 0.005 0.101 3848 Dihedral : 4.484 45.347 3036 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.15 % Allowed : 13.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.17), residues: 2740 helix: 1.15 (0.15), residues: 1240 sheet: -0.47 (0.28), residues: 344 loop : -0.11 (0.20), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1085 TYR 0.014 0.001 TYR C 722 PHE 0.022 0.001 PHE C1100 TRP 0.013 0.001 TRP E 607 HIS 0.003 0.001 HIS E 773 Details of bonding type rmsd covalent geometry : bond 0.00239 (21648) covalent geometry : angle 0.65362 (29348) hydrogen bonds : bond 0.03635 ( 995) hydrogen bonds : angle 5.18202 ( 2808) Misc. bond : bond 0.00006 ( 4) ********************** 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 175 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.818 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 616 MET cc_start: 0.7639 (mmm) cc_final: 0.6995 (mmm) REVERT: A 639 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: A 671 MET cc_start: 0.6865 (tpp) cc_final: 0.6541 (tpp) REVERT: A 743 MET cc_start: 0.6365 (tpt) cc_final: 0.5798 (tpt) REVERT: A 804 MET cc_start: 0.9215 (mmp) cc_final: 0.8879 (mmp) REVERT: A 986 ASP cc_start: 0.7571 (t0) cc_final: 0.7298 (t0) REVERT: A 1067 ASP cc_start: 0.7954 (m-30) cc_final: 0.7545 (t70) REVERT: A 1087 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.6845 (pt) REVERT: B 604 MET cc_start: 0.7770 (ptm) cc_final: 0.7377 (ptm) REVERT: B 616 MET cc_start: 0.9007 (mmm) cc_final: 0.8745 (mmm) REVERT: B 641 MET cc_start: 0.7010 (ptm) cc_final: 0.6465 (ptt) REVERT: B 743 MET cc_start: 0.6405 (tpt) cc_final: 0.6064 (tpt) REVERT: B 804 MET cc_start: 0.7312 (mmp) cc_final: 0.7096 (mmp) REVERT: B 1076 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8926 (p) REVERT: C 641 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6334 (ppp) REVERT: C 671 MET cc_start: 0.7473 (tpp) cc_final: 0.7032 (tpp) REVERT: C 690 MET cc_start: 0.9246 (ppp) cc_final: 0.8865 (pmm) REVERT: C 743 MET cc_start: 0.6108 (tpt) cc_final: 0.5829 (tpt) REVERT: C 804 MET cc_start: 0.8042 (mmp) cc_final: 0.7662 (mmp) REVERT: C 1166 MET cc_start: 0.3231 (ttt) cc_final: 0.2700 (ptm) REVERT: E 546 LEU cc_start: 0.8836 (tt) cc_final: 0.8553 (mp) REVERT: E 641 MET cc_start: 0.6863 (ptm) cc_final: 0.5899 (ppp) REVERT: E 671 MET cc_start: 0.3652 (tpp) cc_final: 0.3168 (tpp) REVERT: E 724 MET cc_start: 0.8662 (ptp) cc_final: 0.8270 (mmt) REVERT: E 783 MET cc_start: 0.7282 (tpp) cc_final: 0.7061 (tpp) REVERT: E 784 LEU cc_start: 0.8778 (pp) cc_final: 0.8323 (mm) REVERT: E 854 MET cc_start: 0.6907 (tpt) cc_final: 0.6657 (tpt) REVERT: E 921 MET cc_start: 0.8653 (mmm) cc_final: 0.8436 (mmm) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.1358 time to fit residues: 37.7132 Evaluate side-chains 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 639 PHE 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 1153 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1076 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 641 MET Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 810 MET Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1059 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 249 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 0.0020 chunk 225 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.053127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.044986 restraints weight = 211915.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.046019 restraints weight = 135524.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.046676 restraints weight = 95186.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.047197 restraints weight = 74434.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.047534 restraints weight = 62214.500| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.8652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21652 Z= 0.136 Angle : 0.672 15.970 29348 Z= 0.337 Chirality : 0.043 0.215 3276 Planarity : 0.005 0.087 3848 Dihedral : 4.508 26.918 3032 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.93 % Allowed : 13.87 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2740 helix: 1.07 (0.15), residues: 1236 sheet: -0.44 (0.28), residues: 344 loop : -0.18 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1085 TYR 0.019 0.001 TYR A 723 PHE 0.024 0.002 PHE A 763 TRP 0.013 0.002 TRP B 607 HIS 0.003 0.001 HIS E 773 Details of bonding type rmsd covalent geometry : bond 0.00293 (21648) covalent geometry : angle 0.67156 (29348) hydrogen bonds : bond 0.03748 ( 995) hydrogen bonds : angle 5.25477 ( 2808) Misc. bond : bond 0.00025 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.98 seconds wall clock time: 65 minutes 10.10 seconds (3910.10 seconds total)