Starting phenix.real_space_refine on Wed Jun 18 15:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7o_36044/06_2025/8j7o_36044_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7o_36044/06_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_36044/06_2025/8j7o_36044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7o_36044/06_2025/8j7o_36044.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7o_36044/06_2025/8j7o_36044_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7o_36044/06_2025/8j7o_36044_neut_trim.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 13448 2.51 5 N 3632 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "B" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "C" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "E" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.41, per 1000 atoms: 0.63 Number of scatterers: 21168 At special positions: 0 Unit cell: (161.391, 106.496, 133.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 3940 8.00 N 3632 7.00 C 13448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 16 sheets defined 50.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 540 through 559 removed outlier: 3.815A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.569A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 610 through 619 removed outlier: 3.664A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 655 through 669 removed outlier: 3.569A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 809 through 818 Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 7.345A pdb=" N CYS A 850 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR A 851 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 881 Processing helix chain 'A' and resid 883 through 885 No H-bonds generated for 'chain 'A' and resid 883 through 885' Processing helix chain 'A' and resid 886 through 902 Processing helix chain 'A' and resid 909 through 925 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 962 through 969 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER A 981 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1034 through 1041 Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.816A pdb=" N ILE B 544 " --> pdb=" O GLY B 540 " (cutoff:3.500A) Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 610 through 619 removed outlier: 3.663A pdb=" N MET B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 Processing helix chain 'B' and resid 655 through 669 removed outlier: 3.570A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 719 through 733 Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'B' and resid 778 through 789 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 809 through 818 Processing helix chain 'B' and resid 827 through 845 removed outlier: 3.601A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 853 removed outlier: 7.345A pdb=" N CYS B 850 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR B 851 " --> pdb=" O PHE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 Processing helix chain 'B' and resid 883 through 885 No H-bonds generated for 'chain 'B' and resid 883 through 885' Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'B' and resid 909 through 925 Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 962 through 969 Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER B 981 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1034 through 1041 Processing helix chain 'C' and resid 495 through 511 Processing helix chain 'C' and resid 540 through 559 removed outlier: 3.817A pdb=" N ILE C 544 " --> pdb=" O GLY C 540 " (cutoff:3.500A) Proline residue: C 550 - end of helix Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Proline residue: C 592 - end of helix Processing helix chain 'C' and resid 610 through 619 removed outlier: 3.663A pdb=" N MET C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 Processing helix chain 'C' and resid 655 through 669 removed outlier: 3.569A pdb=" N VAL C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 719 through 733 Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 778 through 789 Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 809 through 818 Processing helix chain 'C' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 853 removed outlier: 7.346A pdb=" N CYS C 850 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR C 851 " --> pdb=" O PHE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 Processing helix chain 'C' and resid 867 through 881 Processing helix chain 'C' and resid 883 through 885 No H-bonds generated for 'chain 'C' and resid 883 through 885' Processing helix chain 'C' and resid 886 through 902 Processing helix chain 'C' and resid 909 through 925 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 962 through 969 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.805A pdb=" N SER C 981 " --> pdb=" O PRO C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 999 Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1029 through 1033 Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'C' and resid 1091 through 1096 removed outlier: 4.215A pdb=" N MET C1095 " --> pdb=" O ASP C1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 511 Processing helix chain 'E' and resid 540 through 559 removed outlier: 3.817A pdb=" N ILE E 544 " --> pdb=" O GLY E 540 " (cutoff:3.500A) Proline residue: E 550 - end of helix Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.568A pdb=" N ILE E 590 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Proline residue: E 592 - end of helix Processing helix chain 'E' and resid 610 through 619 removed outlier: 3.662A pdb=" N MET E 616 " --> pdb=" O PHE E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 634 Processing helix chain 'E' and resid 655 through 669 removed outlier: 3.570A pdb=" N VAL E 659 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 696 Processing helix chain 'E' and resid 719 through 733 Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'E' and resid 778 through 789 Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 809 through 818 Processing helix chain 'E' and resid 827 through 845 removed outlier: 3.600A pdb=" N LEU E 844 " --> pdb=" O GLY E 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR E 845 " --> pdb=" O ALA E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 853 removed outlier: 7.346A pdb=" N CYS E 850 " --> pdb=" O ALA E 847 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR E 851 " --> pdb=" O PHE E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 860 through 865 Processing helix chain 'E' and resid 867 through 881 Processing helix chain 'E' and resid 883 through 885 No H-bonds generated for 'chain 'E' and resid 883 through 885' Processing helix chain 'E' and resid 886 through 902 Processing helix chain 'E' and resid 909 through 925 Processing helix chain 'E' and resid 927 through 934 Processing helix chain 'E' and resid 941 through 950 Processing helix chain 'E' and resid 962 through 969 Processing helix chain 'E' and resid 977 through 982 removed outlier: 3.804A pdb=" N SER E 981 " --> pdb=" O PRO E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 999 Processing helix chain 'E' and resid 1003 through 1013 Processing helix chain 'E' and resid 1013 through 1028 Processing helix chain 'E' and resid 1029 through 1033 Processing helix chain 'E' and resid 1034 through 1041 Processing helix chain 'E' and resid 1091 through 1096 removed outlier: 4.385A pdb=" N MET E1095 " --> pdb=" O ASP E1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.872A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 674 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 703 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 676 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 705 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET A 641 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 677 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 643 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1053 removed outlier: 7.067A pdb=" N LYS A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN A1075 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A1068 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A1073 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 6.948A pdb=" N ILE A1112 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A1174 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A1160 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A1139 " --> pdb=" O THR A1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1149 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.938A pdb=" N LEU B 565 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.326A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N GLY B 608 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE B 674 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 703 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 676 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER B 705 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1053 removed outlier: 6.251A pdb=" N GLU B1047 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA B1062 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B1049 " --> pdb=" O ILE B1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B1060 " --> pdb=" O GLU B1049 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU B1051 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B1058 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B1053 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA B1062 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B1075 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B1068 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B1073 " --> pdb=" O LEU B1068 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1111 through 1113 removed outlier: 6.949A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B1174 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL B1160 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B1176 " --> pdb=" O ARG B1158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR B1147 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B1139 " --> pdb=" O THR B1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B1149 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 564 through 567 removed outlier: 8.382A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 674 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 703 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 676 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER C 705 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL C 796 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET C 566 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1047 through 1053 removed outlier: 6.252A pdb=" N GLU C1047 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA C1062 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU C1049 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C1060 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU C1051 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C1058 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C1053 " --> pdb=" O LYS C1056 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN C1075 " --> pdb=" O SER C1066 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C1068 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C1073 " --> pdb=" O LEU C1068 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1111 through 1113 removed outlier: 6.950A pdb=" N ILE C1112 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C1174 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C1160 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1146 through 1150 removed outlier: 6.314A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 603 through 604 removed outlier: 4.266A pdb=" N SER E 603 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 564 " --> pdb=" O VAL E 794 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL E 796 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N MET E 566 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 738 " --> pdb=" O HIS E 769 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS E 771 " --> pdb=" O LEU E 738 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 740 " --> pdb=" O HIS E 771 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 674 " --> pdb=" O GLU E 701 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA E 703 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 676 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER E 705 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET E 641 " --> pdb=" O ARG E 675 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE E 677 " --> pdb=" O MET E 641 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 643 " --> pdb=" O PHE E 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1047 through 1053 removed outlier: 6.252A pdb=" N GLU E1047 " --> pdb=" O ALA E1062 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA E1062 " --> pdb=" O GLU E1047 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU E1049 " --> pdb=" O ILE E1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E1060 " --> pdb=" O GLU E1049 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU E1051 " --> pdb=" O LEU E1058 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E1058 " --> pdb=" O GLU E1051 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU E1053 " --> pdb=" O LYS E1056 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA E1062 " --> pdb=" O GLU E1079 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU E1079 " --> pdb=" O ALA E1062 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E1075 " --> pdb=" O SER E1066 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU E1068 " --> pdb=" O GLN E1073 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN E1073 " --> pdb=" O LEU E1068 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1111 through 1113 removed outlier: 6.948A pdb=" N ILE E1112 " --> pdb=" O ILE E1174 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E1174 " --> pdb=" O VAL E1160 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL E1160 " --> pdb=" O ILE E1174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E1176 " --> pdb=" O ARG E1158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1146 through 1150 removed outlier: 6.315A pdb=" N THR E1147 " --> pdb=" O VAL E1139 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL E1139 " --> pdb=" O THR E1147 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL E1149 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU E1137 " --> pdb=" O ILE E1123 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE E1123 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL E1139 " --> pdb=" O ILE E1121 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 6.36 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: 0.05 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.250 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2740 helix: 0.18 (0.13), residues: 1216 sheet: -0.50 (0.28), residues: 328 loop : -0.24 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP B 624 HIS 0.029 0.004 HIS B 771 PHE 0.053 0.010 PHE A 618 TYR 0.097 0.016 TYR E 593 ARG 0.018 0.001 ARG A 732 Details of bonding type rmsd hydrogen bonds : bond 0.18320 ( 995) hydrogen bonds : angle 7.83109 ( 2808) covalent geometry : bond 0.01202 (21648) covalent geometry : angle 1.60271 (29348) 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 : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6718 (mp) REVERT: E 606 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6141 (p0) REVERT: E 783 MET cc_start: 0.7424 (mmp) cc_final: 0.7216 (mmp) REVERT: E 1166 MET cc_start: 0.2997 (ttt) cc_final: 0.2598 (mtp) outliers start: 60 outliers final: 12 residues processed: 400 average time/residue: 0.4148 time to fit residues: 240.7622 Evaluate side-chains 192 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN A 807 GLN A 998 HIS ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN A1135 GLN B 807 GLN B 998 HIS B1075 GLN B1135 GLN C 807 GLN C1075 GLN C1135 GLN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.063759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.054568 restraints weight = 195933.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.055852 restraints weight = 131494.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.056771 restraints weight = 95426.386| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21652 Z= 0.180 Angle : 0.718 14.471 29348 Z= 0.365 Chirality : 0.045 0.195 3276 Planarity : 0.005 0.053 3848 Dihedral : 6.862 70.003 3077 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.68 % Allowed : 9.50 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2740 helix: 1.48 (0.15), residues: 1208 sheet: -0.26 (0.27), residues: 368 loop : 0.36 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 838 HIS 0.008 0.002 HIS C1161 PHE 0.029 0.002 PHE A1078 TYR 0.020 0.002 TYR E 503 ARG 0.013 0.001 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 995) hydrogen bonds : angle 5.71413 ( 2808) covalent geometry : bond 0.00387 (21648) covalent geometry : angle 0.71841 (29348) Misc. bond : bond 0.00364 ( 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 219 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8851 (mpp) REVERT: A 804 MET cc_start: 0.8989 (mmp) cc_final: 0.8392 (mmp) REVERT: A 921 MET cc_start: 0.7808 (mmm) cc_final: 0.7541 (mmm) REVERT: A 986 ASP cc_start: 0.7797 (t0) cc_final: 0.7568 (t0) REVERT: B 607 TRP cc_start: 0.6056 (OUTLIER) cc_final: 0.4976 (t60) REVERT: B 641 MET cc_start: 0.7673 (ptm) cc_final: 0.6776 (ptm) REVERT: B 804 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7451 (mmp) REVERT: B 810 MET cc_start: 0.5718 (tmm) cc_final: 0.5446 (tmm) REVERT: B 854 MET cc_start: 0.6390 (tmm) cc_final: 0.5493 (ppp) REVERT: B 1058 LEU cc_start: 0.9475 (tp) cc_final: 0.9196 (tp) REVERT: C 500 LEU cc_start: 0.9428 (mt) cc_final: 0.9187 (mt) REVERT: C 743 MET cc_start: 0.4804 (tpt) cc_final: 0.4421 (tpt) REVERT: C 756 VAL cc_start: 0.8254 (t) cc_final: 0.8047 (t) REVERT: C 854 MET cc_start: 0.6962 (ppp) cc_final: 0.6379 (tmm) REVERT: E 641 MET cc_start: 0.6100 (ptm) cc_final: 0.5673 (ppp) REVERT: E 671 MET cc_start: 0.4247 (tpp) cc_final: 0.3825 (tpp) REVERT: E 724 MET cc_start: 0.7546 (ptm) cc_final: 0.6842 (mmt) REVERT: E 784 LEU cc_start: 0.8277 (pp) cc_final: 0.7655 (mm) REVERT: E 921 MET cc_start: 0.7880 (mmm) cc_final: 0.7498 (mmm) REVERT: E 1166 MET cc_start: 0.2612 (ttt) cc_final: 0.2403 (mtp) outliers start: 38 outliers final: 18 residues processed: 210 average time/residue: 0.3315 time to fit residues: 109.3236 Evaluate side-chains 172 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1059 HIS Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 766 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 836 GLU Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 191 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 160 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS E 510 ASN E 647 ASN E1073 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.056323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.047785 restraints weight = 204064.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.048856 restraints weight = 135668.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.049523 restraints weight = 98440.175| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 21652 Z= 0.251 Angle : 0.820 16.814 29348 Z= 0.421 Chirality : 0.048 0.209 3276 Planarity : 0.007 0.096 3848 Dihedral : 6.478 58.535 3068 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.83 % Allowed : 9.85 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2740 helix: 0.47 (0.14), residues: 1216 sheet: -0.58 (0.26), residues: 388 loop : -0.15 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP C 607 HIS 0.007 0.002 HIS C 998 PHE 0.047 0.003 PHE B1100 TYR 0.022 0.003 TYR E1013 ARG 0.013 0.001 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.05455 ( 995) hydrogen bonds : angle 5.65608 ( 2808) covalent geometry : bond 0.00538 (21648) covalent geometry : angle 0.81993 (29348) Misc. bond : bond 0.00044 ( 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 229 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 165 time to evaluate : 2.417 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 686 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8887 (mpp) REVERT: A 804 MET cc_start: 0.9167 (mmp) cc_final: 0.8613 (mmp) REVERT: A 986 ASP cc_start: 0.7567 (t0) cc_final: 0.7268 (t0) REVERT: B 616 MET cc_start: 0.8959 (mmm) cc_final: 0.8643 (mmm) REVERT: B 854 MET cc_start: 0.7354 (tmm) cc_final: 0.7083 (ppp) REVERT: B 986 ASP cc_start: 0.8522 (t0) cc_final: 0.8288 (t0) REVERT: B 1076 VAL cc_start: 0.9218 (t) cc_final: 0.8987 (p) REVERT: C 496 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8123 (mmm160) REVERT: C 616 MET cc_start: 0.8821 (mpp) cc_final: 0.8513 (mmt) REVERT: C 621 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: C 641 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6886 (ppp) REVERT: C 671 MET cc_start: 0.7860 (tpp) cc_final: 0.7456 (tpp) REVERT: C 743 MET cc_start: 0.5237 (tpt) cc_final: 0.4687 (tpt) REVERT: C 804 MET cc_start: 0.8257 (mmp) cc_final: 0.7934 (mmp) REVERT: C 921 MET cc_start: 0.7838 (mmm) cc_final: 0.7506 (mmm) REVERT: E 571 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6200 (ttp80) REVERT: E 641 MET cc_start: 0.7067 (ptm) cc_final: 0.6238 (ptm) REVERT: E 724 MET cc_start: 0.8500 (ptm) cc_final: 0.8067 (mmt) REVERT: E 1101 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8971 (p-80) REVERT: E 1166 MET cc_start: 0.2618 (ttt) cc_final: 0.2298 (mtp) outliers start: 64 outliers final: 25 residues processed: 214 average time/residue: 0.3489 time to fit residues: 115.3669 Evaluate side-chains 176 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 1024 THR 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 621 GLU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 605 GLU 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 997 ARG Chi-restraints excluded: chain E residue 1024 THR Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1073 GLN Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 246 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 ASN ** B 669 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.056743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.048010 restraints weight = 204662.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.049133 restraints weight = 133524.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.049843 restraints weight = 95224.009| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21652 Z= 0.141 Angle : 0.626 16.719 29348 Z= 0.316 Chirality : 0.043 0.156 3276 Planarity : 0.005 0.062 3848 Dihedral : 5.548 59.192 3050 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.86 % Allowed : 11.44 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2740 helix: 0.99 (0.15), residues: 1220 sheet: -0.63 (0.27), residues: 384 loop : -0.05 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 607 HIS 0.004 0.001 HIS A 875 PHE 0.026 0.002 PHE E1078 TYR 0.014 0.002 TYR C 722 ARG 0.009 0.001 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 995) hydrogen bonds : angle 5.27151 ( 2808) covalent geometry : bond 0.00300 (21648) covalent geometry : angle 0.62631 (29348) Misc. bond : bond 0.00027 ( 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 196 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 2.576 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: A 686 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9047 (mpp) REVERT: A 804 MET cc_start: 0.9223 (mmp) cc_final: 0.8803 (mmp) REVERT: A 986 ASP cc_start: 0.7520 (t0) cc_final: 0.7219 (t0) REVERT: A 1087 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5203 (pt) REVERT: B 616 MET cc_start: 0.8998 (mmm) cc_final: 0.8720 (mmm) REVERT: B 641 MET cc_start: 0.7509 (ptm) cc_final: 0.6994 (ptm) REVERT: B 686 MET cc_start: 0.9354 (mpp) cc_final: 0.9033 (mpp) REVERT: B 743 MET cc_start: 0.6169 (tpt) cc_final: 0.5763 (tpt) REVERT: B 986 ASP cc_start: 0.8499 (t0) cc_final: 0.8227 (t0) REVERT: B 1076 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 496 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7921 (mmm160) REVERT: C 616 MET cc_start: 0.9142 (mpp) cc_final: 0.8884 (mpp) REVERT: C 621 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8636 (tp30) REVERT: C 743 MET cc_start: 0.5288 (tpt) cc_final: 0.4660 (tpt) REVERT: C 804 MET cc_start: 0.8370 (mmp) cc_final: 0.7971 (mmp) REVERT: C 921 MET cc_start: 0.7830 (mmm) cc_final: 0.7422 (mmm) REVERT: C 1046 GLU cc_start: 0.8983 (tt0) cc_final: 0.8779 (tt0) REVERT: C 1098 MET cc_start: 0.5412 (tpt) cc_final: 0.4495 (tpt) REVERT: C 1116 MET cc_start: 0.4827 (ptp) cc_final: 0.4620 (ptp) REVERT: C 1166 MET cc_start: 0.4164 (tmm) cc_final: 0.3866 (ptm) REVERT: E 508 MET cc_start: 0.9274 (tpp) cc_final: 0.8855 (tpp) REVERT: E 641 MET cc_start: 0.7152 (ptm) cc_final: 0.6505 (ptm) REVERT: E 724 MET cc_start: 0.8389 (ptm) cc_final: 0.7931 (mmt) REVERT: E 1047 GLU cc_start: 0.9559 (tt0) cc_final: 0.9325 (tp30) REVERT: E 1098 MET cc_start: 0.7438 (tpt) cc_final: 0.7187 (tpt) REVERT: E 1166 MET cc_start: 0.2860 (ttt) cc_final: 0.2548 (mtp) outliers start: 42 outliers final: 23 residues processed: 185 average time/residue: 0.3281 time to fit residues: 95.4407 Evaluate side-chains 176 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 621 GLU 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 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 604 MET 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 621 GLU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG 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 1073 GLN Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 32 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS A1135 GLN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN E 875 HIS E1073 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.054553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.046174 restraints weight = 209180.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.047230 restraints weight = 137702.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.047988 restraints weight = 98078.081| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21652 Z= 0.189 Angle : 0.675 12.838 29348 Z= 0.344 Chirality : 0.043 0.162 3276 Planarity : 0.005 0.050 3848 Dihedral : 5.579 58.851 3050 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.99 % Allowed : 12.19 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2740 helix: 0.75 (0.14), residues: 1224 sheet: -0.66 (0.26), residues: 392 loop : -0.13 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 607 HIS 0.007 0.001 HIS A 875 PHE 0.025 0.002 PHE E1078 TYR 0.014 0.002 TYR C 722 ARG 0.009 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 995) hydrogen bonds : angle 5.38136 ( 2808) covalent geometry : bond 0.00397 (21648) covalent geometry : angle 0.67507 (29348) 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 199 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 2.248 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 671 MET cc_start: 0.6912 (tpp) cc_final: 0.6321 (tpp) REVERT: A 743 MET cc_start: 0.6026 (tpt) cc_final: 0.5816 (tpt) REVERT: A 804 MET cc_start: 0.9227 (mmp) cc_final: 0.8918 (mmp) REVERT: A 921 MET cc_start: 0.8286 (mmm) cc_final: 0.8084 (mmm) REVERT: A 986 ASP cc_start: 0.7562 (t0) cc_final: 0.7279 (t0) REVERT: A 1087 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6336 (pt) REVERT: B 616 MET cc_start: 0.9010 (mmm) cc_final: 0.8734 (mmm) REVERT: B 743 MET cc_start: 0.6298 (tpt) cc_final: 0.5771 (tpt) REVERT: B 804 MET cc_start: 0.7233 (mmp) cc_final: 0.6616 (mmp) REVERT: B 854 MET cc_start: 0.6491 (ttt) cc_final: 0.5717 (tmm) REVERT: B 921 MET cc_start: 0.8977 (mmm) cc_final: 0.8692 (mmm) REVERT: B 986 ASP cc_start: 0.8419 (t0) cc_final: 0.8144 (t70) REVERT: C 616 MET cc_start: 0.9184 (mpp) cc_final: 0.8861 (mpp) REVERT: C 641 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6600 (ppp) REVERT: C 671 MET cc_start: 0.7636 (tpp) cc_final: 0.7293 (tpp) REVERT: C 743 MET cc_start: 0.5588 (tpt) cc_final: 0.4824 (tpt) REVERT: C 854 MET cc_start: 0.7430 (ppp) cc_final: 0.6804 (ppp) REVERT: C 921 MET cc_start: 0.7998 (mmm) cc_final: 0.7749 (mmm) REVERT: C 1098 MET cc_start: 0.5065 (tpt) cc_final: 0.4300 (tpt) REVERT: C 1166 MET cc_start: 0.4205 (tmm) cc_final: 0.3874 (ptm) REVERT: E 500 LEU cc_start: 0.9123 (mt) cc_final: 0.8884 (mt) REVERT: E 571 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6633 (ttp80) REVERT: E 671 MET cc_start: 0.4902 (tpp) cc_final: 0.4581 (tpp) REVERT: E 724 MET cc_start: 0.8526 (ptm) cc_final: 0.8205 (mmt) REVERT: E 921 MET cc_start: 0.8471 (mmm) cc_final: 0.7972 (mmm) outliers start: 45 outliers final: 25 residues processed: 187 average time/residue: 0.3203 time to fit residues: 95.8869 Evaluate side-chains 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 621 GLU 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 B residue 496 ARG Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1101 HIS 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 641 MET Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1000 GLU Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 905 ILE Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 140 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS C 647 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.054069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.045738 restraints weight = 208324.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.046785 restraints weight = 135497.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.047499 restraints weight = 96284.430| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21652 Z= 0.152 Angle : 0.642 13.971 29348 Z= 0.323 Chirality : 0.043 0.168 3276 Planarity : 0.005 0.050 3848 Dihedral : 5.395 57.294 3050 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.81 % Allowed : 12.59 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2740 helix: 0.88 (0.15), residues: 1224 sheet: -0.66 (0.26), residues: 392 loop : -0.08 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 838 HIS 0.004 0.001 HIS A 875 PHE 0.020 0.002 PHE E1100 TYR 0.020 0.002 TYR B 722 ARG 0.006 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 995) hydrogen bonds : angle 5.26765 ( 2808) covalent geometry : bond 0.00314 (21648) covalent geometry : angle 0.64178 (29348) 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 189 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 2.477 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 743 MET cc_start: 0.6255 (tpt) cc_final: 0.6022 (tpt) REVERT: A 804 MET cc_start: 0.9181 (mmp) cc_final: 0.8928 (mmp) REVERT: A 881 MET cc_start: 0.8828 (mmt) cc_final: 0.8483 (mmp) REVERT: A 986 ASP cc_start: 0.7491 (t0) cc_final: 0.7219 (t0) REVERT: A 1067 ASP cc_start: 0.8006 (m-30) cc_final: 0.7619 (t70) REVERT: A 1087 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.6733 (pt) REVERT: A 1095 MET cc_start: 0.7047 (pmm) cc_final: 0.6758 (pmm) REVERT: B 616 MET cc_start: 0.9003 (mmm) cc_final: 0.8779 (mmm) REVERT: B 671 MET cc_start: 0.7022 (tpp) cc_final: 0.6593 (tpp) REVERT: B 743 MET cc_start: 0.6405 (tpt) cc_final: 0.5951 (tpt) REVERT: B 804 MET cc_start: 0.7298 (mmp) cc_final: 0.6903 (mmp) REVERT: B 986 ASP cc_start: 0.8429 (t0) cc_final: 0.8152 (t70) REVERT: C 496 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8602 (mmp-170) REVERT: C 616 MET cc_start: 0.9163 (mpp) cc_final: 0.8941 (mmm) REVERT: C 671 MET cc_start: 0.7557 (tpp) cc_final: 0.7184 (tpp) REVERT: C 743 MET cc_start: 0.5709 (tpt) cc_final: 0.4973 (tpt) REVERT: C 804 MET cc_start: 0.8042 (mmp) cc_final: 0.7588 (mmp) REVERT: C 921 MET cc_start: 0.8152 (mmm) cc_final: 0.7942 (mmm) REVERT: C 1098 MET cc_start: 0.5143 (tpt) cc_final: 0.4325 (tpt) REVERT: C 1153 MET cc_start: 0.4754 (tmm) cc_final: 0.4252 (tmm) REVERT: E 500 LEU cc_start: 0.9218 (mt) cc_final: 0.8993 (mt) REVERT: E 508 MET cc_start: 0.9226 (tpt) cc_final: 0.8972 (tpp) REVERT: E 566 MET cc_start: 0.7617 (tpt) cc_final: 0.6987 (tpt) REVERT: E 641 MET cc_start: 0.7707 (ptm) cc_final: 0.7432 (ptm) REVERT: E 724 MET cc_start: 0.8556 (ptm) cc_final: 0.8237 (mmt) REVERT: E 921 MET cc_start: 0.8715 (mmm) cc_final: 0.8343 (mmm) REVERT: E 1169 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9151 (mp0) outliers start: 41 outliers final: 21 residues processed: 179 average time/residue: 0.3539 time to fit residues: 100.9779 Evaluate side-chains 169 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain B residue 903 ASP 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 836 GLU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 828 MET 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 1169 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.051123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.043286 restraints weight = 216270.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.044278 restraints weight = 139520.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.044970 restraints weight = 98732.211| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21652 Z= 0.222 Angle : 0.776 17.666 29348 Z= 0.391 Chirality : 0.046 0.225 3276 Planarity : 0.006 0.060 3848 Dihedral : 5.738 56.680 3046 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.81 % Allowed : 13.12 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2740 helix: 0.31 (0.14), residues: 1216 sheet: -0.64 (0.27), residues: 388 loop : -0.45 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 624 HIS 0.007 0.002 HIS E1019 PHE 0.030 0.003 PHE E1100 TYR 0.017 0.002 TYR A 871 ARG 0.009 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 995) hydrogen bonds : angle 5.62270 ( 2808) covalent geometry : bond 0.00466 (21648) covalent geometry : angle 0.77557 (29348) Misc. bond : bond 0.00011 ( 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 192 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 MET cc_start: 0.9139 (mmp) cc_final: 0.8922 (mmp) REVERT: A 881 MET cc_start: 0.8928 (mmt) cc_final: 0.8721 (mmp) REVERT: A 986 ASP cc_start: 0.7605 (t0) cc_final: 0.7319 (t0) REVERT: A 1067 ASP cc_start: 0.8128 (m-30) cc_final: 0.7682 (t70) REVERT: A 1087 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7258 (pt) REVERT: B 616 MET cc_start: 0.9074 (mmm) cc_final: 0.8802 (mmm) REVERT: B 641 MET cc_start: 0.7203 (ptm) cc_final: 0.6641 (ptm) REVERT: B 743 MET cc_start: 0.6593 (tpt) cc_final: 0.6095 (tpt) REVERT: B 754 MET cc_start: 0.8856 (ttp) cc_final: 0.8553 (ptp) REVERT: B 804 MET cc_start: 0.7629 (mmp) cc_final: 0.7380 (mmp) REVERT: B 921 MET cc_start: 0.9083 (mmm) cc_final: 0.8853 (mmm) REVERT: B 1058 LEU cc_start: 0.9587 (tp) cc_final: 0.9354 (pp) REVERT: C 616 MET cc_start: 0.9143 (mpp) cc_final: 0.8769 (mpp) REVERT: C 686 MET cc_start: 0.9124 (mtm) cc_final: 0.8769 (mpp) REVERT: C 804 MET cc_start: 0.8082 (mmp) cc_final: 0.7825 (mmp) REVERT: C 921 MET cc_start: 0.8242 (mmm) cc_final: 0.7996 (mmm) REVERT: E 566 MET cc_start: 0.6827 (tpt) cc_final: 0.6427 (tpt) REVERT: E 641 MET cc_start: 0.8082 (ptm) cc_final: 0.7369 (ptm) REVERT: E 724 MET cc_start: 0.8758 (ptm) cc_final: 0.8455 (mmt) REVERT: E 921 MET cc_start: 0.8930 (mmm) cc_final: 0.8676 (mmm) REVERT: E 970 ASP cc_start: 0.8908 (m-30) cc_final: 0.8437 (p0) REVERT: E 1098 MET cc_start: 0.7893 (tpt) cc_final: 0.7469 (tpt) outliers start: 41 outliers final: 23 residues processed: 179 average time/residue: 0.3417 time to fit residues: 97.8696 Evaluate side-chains 166 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE 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 1101 HIS Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 828 MET Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 997 ARG Chi-restraints excluded: chain E residue 1024 THR Chi-restraints excluded: chain E residue 1059 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 27 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 269 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN B 669 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN E1075 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.052373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.044402 restraints weight = 210375.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.045445 restraints weight = 133256.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.046121 restraints weight = 93159.983| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.8758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21652 Z= 0.129 Angle : 0.665 13.168 29348 Z= 0.328 Chirality : 0.044 0.267 3276 Planarity : 0.005 0.067 3848 Dihedral : 5.250 56.015 3042 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.24 % Allowed : 13.91 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2740 helix: 0.77 (0.15), residues: 1216 sheet: -0.70 (0.26), residues: 384 loop : -0.22 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 607 HIS 0.003 0.001 HIS E 773 PHE 0.040 0.002 PHE A1100 TYR 0.015 0.001 TYR B 722 ARG 0.012 0.001 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 995) hydrogen bonds : angle 5.29532 ( 2808) covalent geometry : bond 0.00271 (21648) covalent geometry : angle 0.66484 (29348) Misc. bond : bond 0.00019 ( 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 179 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 2.208 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 743 MET cc_start: 0.6621 (tpt) cc_final: 0.5962 (tpt) REVERT: A 881 MET cc_start: 0.9015 (mmt) cc_final: 0.8807 (mmp) REVERT: A 921 MET cc_start: 0.8611 (mmm) cc_final: 0.8177 (mpp) REVERT: A 986 ASP cc_start: 0.7429 (t0) cc_final: 0.7166 (t0) REVERT: A 1067 ASP cc_start: 0.8131 (m-30) cc_final: 0.7738 (t70) REVERT: A 1087 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7168 (pt) REVERT: B 616 MET cc_start: 0.9074 (mmm) cc_final: 0.8809 (mmm) REVERT: B 641 MET cc_start: 0.6865 (ptm) cc_final: 0.6604 (ptt) REVERT: B 686 MET cc_start: 0.9330 (mpp) cc_final: 0.8926 (mpp) REVERT: B 690 MET cc_start: 0.9037 (ptp) cc_final: 0.8783 (tmm) REVERT: B 743 MET cc_start: 0.6547 (tpt) cc_final: 0.6191 (tpt) REVERT: B 754 MET cc_start: 0.8891 (ttp) cc_final: 0.8618 (ptp) REVERT: B 801 MET cc_start: 0.8462 (mmm) cc_final: 0.8223 (mmm) REVERT: B 804 MET cc_start: 0.7573 (mmp) cc_final: 0.7343 (mmp) REVERT: B 921 MET cc_start: 0.9172 (mmm) cc_final: 0.8937 (mmm) REVERT: B 986 ASP cc_start: 0.8330 (t0) cc_final: 0.7924 (t0) REVERT: C 743 MET cc_start: 0.6281 (tpt) cc_final: 0.5486 (tpt) REVERT: C 804 MET cc_start: 0.8222 (mmp) cc_final: 0.7894 (mmp) REVERT: C 854 MET cc_start: 0.7435 (ppp) cc_final: 0.6253 (ppp) REVERT: C 921 MET cc_start: 0.8319 (mmm) cc_final: 0.7915 (mmm) REVERT: E 508 MET cc_start: 0.9234 (tpp) cc_final: 0.8865 (tpp) REVERT: E 566 MET cc_start: 0.7126 (tpt) cc_final: 0.6876 (tpt) REVERT: E 641 MET cc_start: 0.7956 (ptm) cc_final: 0.7291 (ptm) REVERT: E 724 MET cc_start: 0.8641 (ptm) cc_final: 0.8419 (mmt) REVERT: E 801 MET cc_start: 0.8701 (mmm) cc_final: 0.8495 (mmm) REVERT: E 921 MET cc_start: 0.8965 (mmm) cc_final: 0.8612 (mmm) REVERT: E 1098 MET cc_start: 0.7683 (tpt) cc_final: 0.7333 (tpt) outliers start: 28 outliers final: 14 residues processed: 174 average time/residue: 0.3012 time to fit residues: 86.0292 Evaluate side-chains 160 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 501 LEU 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 1087 ILE Chi-restraints excluded: chain E residue 1101 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 25 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN B 606 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.052016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.044138 restraints weight = 209836.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.045120 restraints weight = 133424.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.045820 restraints weight = 93880.073| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.8985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21652 Z= 0.133 Angle : 0.675 18.537 29348 Z= 0.331 Chirality : 0.043 0.206 3276 Planarity : 0.005 0.061 3848 Dihedral : 5.174 53.918 3042 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.97 % Allowed : 13.74 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2740 helix: 0.87 (0.15), residues: 1216 sheet: -0.64 (0.27), residues: 384 loop : -0.21 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 607 HIS 0.006 0.001 HIS A1101 PHE 0.028 0.002 PHE A 763 TYR 0.011 0.001 TYR B 722 ARG 0.012 0.001 ARG C1085 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 995) hydrogen bonds : angle 5.29062 ( 2808) covalent geometry : bond 0.00286 (21648) covalent geometry : angle 0.67530 (29348) Misc. bond : bond 0.00020 ( 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 169 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 MET cc_start: 0.6633 (tpt) cc_final: 0.6012 (tpt) REVERT: A 921 MET cc_start: 0.8632 (mmm) cc_final: 0.8286 (mmm) REVERT: A 986 ASP cc_start: 0.7547 (t0) cc_final: 0.7286 (t0) REVERT: A 1067 ASP cc_start: 0.8155 (m-30) cc_final: 0.7743 (t70) REVERT: A 1087 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7228 (pt) REVERT: B 616 MET cc_start: 0.9085 (mmm) cc_final: 0.8817 (mmm) REVERT: B 641 MET cc_start: 0.6910 (ptm) cc_final: 0.6594 (ptt) REVERT: B 690 MET cc_start: 0.9079 (ptp) cc_final: 0.8831 (tmm) REVERT: B 743 MET cc_start: 0.6975 (tpt) cc_final: 0.6562 (tpt) REVERT: B 754 MET cc_start: 0.8919 (ttp) cc_final: 0.8642 (ptp) REVERT: B 783 MET cc_start: 0.7697 (tpp) cc_final: 0.7461 (tpp) REVERT: B 804 MET cc_start: 0.7598 (mmp) cc_final: 0.7365 (mmp) REVERT: B 921 MET cc_start: 0.9197 (mmm) cc_final: 0.8954 (mmm) REVERT: B 986 ASP cc_start: 0.8336 (t0) cc_final: 0.7914 (t0) REVERT: C 616 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: C 743 MET cc_start: 0.6527 (tpt) cc_final: 0.6111 (tpt) REVERT: C 804 MET cc_start: 0.8169 (mmp) cc_final: 0.7852 (mmp) REVERT: C 854 MET cc_start: 0.7454 (ppp) cc_final: 0.6257 (ppp) REVERT: C 921 MET cc_start: 0.8358 (mmm) cc_final: 0.8150 (mmm) REVERT: C 1022 ASP cc_start: 0.8821 (m-30) cc_final: 0.8439 (t0) REVERT: E 508 MET cc_start: 0.9230 (tpp) cc_final: 0.8822 (tpp) REVERT: E 546 LEU cc_start: 0.8935 (tt) cc_final: 0.8650 (pp) REVERT: E 566 MET cc_start: 0.7148 (tpt) cc_final: 0.6899 (tpt) REVERT: E 641 MET cc_start: 0.8017 (ptm) cc_final: 0.7336 (ptm) REVERT: E 724 MET cc_start: 0.8672 (ptm) cc_final: 0.8458 (mmt) REVERT: E 783 MET cc_start: 0.6962 (tpp) cc_final: 0.6720 (tpp) REVERT: E 854 MET cc_start: 0.6977 (tpt) cc_final: 0.6650 (tpt) REVERT: E 921 MET cc_start: 0.8968 (mmm) cc_final: 0.8660 (mmm) outliers start: 22 outliers final: 15 residues processed: 163 average time/residue: 0.3007 time to fit residues: 81.0480 Evaluate side-chains 163 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain B residue 496 ARG 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 616 MET Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1087 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 0.2980 chunk 12 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.052578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.044641 restraints weight = 208287.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.045642 restraints weight = 132224.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.046301 restraints weight = 92234.447| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.9049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21652 Z= 0.110 Angle : 0.676 17.753 29348 Z= 0.327 Chirality : 0.043 0.198 3276 Planarity : 0.005 0.050 3848 Dihedral : 4.539 28.214 3032 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.75 % Allowed : 14.13 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2740 helix: 0.98 (0.15), residues: 1220 sheet: -0.55 (0.27), residues: 388 loop : -0.15 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 607 HIS 0.004 0.001 HIS E 771 PHE 0.025 0.002 PHE A1100 TYR 0.012 0.001 TYR B 722 ARG 0.011 0.000 ARG C1085 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 995) hydrogen bonds : angle 5.18098 ( 2808) covalent geometry : bond 0.00236 (21648) covalent geometry : angle 0.67574 (29348) Misc. bond : bond 0.00025 ( 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 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6808 (mmp80) REVERT: A 743 MET cc_start: 0.6607 (tpt) cc_final: 0.5970 (tpt) REVERT: A 854 MET cc_start: 0.6564 (ttt) cc_final: 0.5760 (ppp) REVERT: A 921 MET cc_start: 0.8531 (mmm) cc_final: 0.8119 (mpp) REVERT: A 986 ASP cc_start: 0.7419 (t0) cc_final: 0.7151 (t0) REVERT: A 1067 ASP cc_start: 0.8155 (m-30) cc_final: 0.7763 (t70) REVERT: A 1077 PHE cc_start: 0.8313 (m-80) cc_final: 0.8096 (m-80) REVERT: A 1087 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7121 (pt) REVERT: B 616 MET cc_start: 0.9119 (mmm) cc_final: 0.8835 (mmm) REVERT: B 641 MET cc_start: 0.6744 (ptm) cc_final: 0.6523 (ptt) REVERT: B 686 MET cc_start: 0.9402 (mpp) cc_final: 0.9021 (mpp) REVERT: B 690 MET cc_start: 0.9054 (ptp) cc_final: 0.8844 (tmm) REVERT: B 743 MET cc_start: 0.6997 (tpt) cc_final: 0.6620 (tpt) REVERT: B 754 MET cc_start: 0.8896 (ttp) cc_final: 0.8638 (ptp) REVERT: B 801 MET cc_start: 0.8431 (mmm) cc_final: 0.8167 (mmm) REVERT: B 804 MET cc_start: 0.7561 (mmp) cc_final: 0.7312 (mmp) REVERT: B 986 ASP cc_start: 0.8283 (t0) cc_final: 0.7878 (t0) REVERT: C 616 MET cc_start: 0.8805 (mmm) cc_final: 0.8482 (mmm) REVERT: C 686 MET cc_start: 0.9305 (mtm) cc_final: 0.8951 (mpp) REVERT: C 743 MET cc_start: 0.6478 (tpt) cc_final: 0.6133 (tpt) REVERT: C 804 MET cc_start: 0.8003 (mmp) cc_final: 0.7708 (mmp) REVERT: C 854 MET cc_start: 0.7394 (ppp) cc_final: 0.6183 (ppp) REVERT: C 1022 ASP cc_start: 0.8742 (m-30) cc_final: 0.8396 (t0) REVERT: E 508 MET cc_start: 0.9220 (tpp) cc_final: 0.8777 (tpp) REVERT: E 546 LEU cc_start: 0.8911 (tt) cc_final: 0.8636 (pp) REVERT: E 641 MET cc_start: 0.7911 (ptm) cc_final: 0.7264 (ptm) REVERT: E 724 MET cc_start: 0.8659 (ptm) cc_final: 0.8389 (mmt) REVERT: E 783 MET cc_start: 0.7018 (tpp) cc_final: 0.6794 (tpp) REVERT: E 854 MET cc_start: 0.6850 (tpt) cc_final: 0.6505 (tpt) REVERT: E 1087 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6994 (mm) outliers start: 17 outliers final: 11 residues processed: 163 average time/residue: 0.3015 time to fit residues: 80.3744 Evaluate side-chains 159 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1087 ILE 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 1016 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 1059 HIS Chi-restraints excluded: chain E residue 1087 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 46 optimal weight: 0.0030 chunk 137 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.051967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.044101 restraints weight = 210828.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.045115 restraints weight = 132612.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.045788 restraints weight = 92972.337| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.9285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21652 Z= 0.130 Angle : 0.673 16.145 29348 Z= 0.330 Chirality : 0.043 0.179 3276 Planarity : 0.005 0.052 3848 Dihedral : 4.566 28.920 3032 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.88 % Allowed : 13.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2740 helix: 0.86 (0.15), residues: 1240 sheet: -0.27 (0.29), residues: 356 loop : -0.22 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 607 HIS 0.003 0.001 HIS E 773 PHE 0.022 0.002 PHE A 763 TYR 0.011 0.001 TYR C 837 ARG 0.010 0.000 ARG C1085 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 995) hydrogen bonds : angle 5.26226 ( 2808) covalent geometry : bond 0.00281 (21648) covalent geometry : angle 0.67282 (29348) Misc. bond : bond 0.00020 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7527.15 seconds wall clock time: 134 minutes 42.91 seconds (8082.91 seconds total)