Starting phenix.real_space_refine on Mon Sep 14 20:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9j_8785/09_2026/5w9j_8785.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 180 5.16 5 C 20904 2.51 5 N 5475 2.21 5 O 6399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32958 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "K" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "L" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 6.67, per 1000 atoms: 0.20 Number of scatterers: 32958 At special positions: 0 Unit cell: (155.04, 154.02, 191.76, 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 180 16.00 O 6399 8.00 N 5475 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.09 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.12 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.09 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.12 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.09 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.12 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.10 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.07 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.83 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.04 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.09 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.21 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.28 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.02 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.09 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.10 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.07 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.84 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.03 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.04 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.09 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.21 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.28 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=2.02 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=2.09 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.10 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.07 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.84 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.03 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.04 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=2.09 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=2.22 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=2.28 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=2.02 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.09 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=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 75 sheets defined 22.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.832A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 908 through 913 Processing helix chain 'D' and resid 926 through 931 removed outlier: 3.627A pdb=" N ALA D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 984 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1011 Processing helix chain 'D' and resid 1016 through 1040 removed outlier: 3.551A pdb=" N LEU D1033 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D1040 " --> pdb=" O LEU D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1057 Processing helix chain 'D' and resid 1059 through 1107 Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.991A pdb=" N GLY E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.831A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.626A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.550A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.990A pdb=" N GLY B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'G' and resid 816 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.831A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 913 Processing helix chain 'G' and resid 926 through 931 removed outlier: 3.626A pdb=" N ALA G 930 " --> pdb=" O ALA G 926 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 984 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1011 Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.550A pdb=" N LEU G1033 " --> pdb=" O ASN G1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1057 Processing helix chain 'G' and resid 1059 through 1107 Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.991A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.868A pdb=" N ASP J 41 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.628A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 416 removed outlier: 3.647A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 436 Processing helix chain 'J' and resid 451 through 455 removed outlier: 3.734A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 676 through 678 No H-bonds generated for 'chain 'J' and resid 676 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.868A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 107 Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 303 through 307 Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.629A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.647A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 451 through 455 removed outlier: 3.733A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 676 through 678 No H-bonds generated for 'chain 'K' and resid 676 through 678' Processing helix chain 'K' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.869A pdb=" N ASP L 41 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 107 Processing helix chain 'L' and resid 133 through 137 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 303 through 307 Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 390 removed outlier: 3.629A pdb=" N SER L 390 " --> pdb=" O PRO L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 416 removed outlier: 3.648A pdb=" N LEU L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 436 Processing helix chain 'L' and resid 451 through 455 removed outlier: 3.733A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 676 through 678 No H-bonds generated for 'chain 'L' and resid 676 through 678' Processing helix chain 'L' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 717 through 724 removed outlier: 7.025A pdb=" N MET D 757 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER J 720 " --> pdb=" O MET D 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU D 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU J 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 737 " --> pdb=" O LEU J 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU J 729 " --> pdb=" O ALA J 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.820A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'D' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'D' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.513A pdb=" N VAL E 16 " --> pdb=" O ARG E 82B" (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG E 82B" --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.061A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 717 through 724 removed outlier: 7.024A pdb=" N MET A 757 " --> pdb=" O VAL K 718 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER K 720 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 737 " --> pdb=" O LEU K 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU K 729 " --> pdb=" O ALA K 737 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.514A pdb=" N VAL B 16 " --> pdb=" O ARG B 82B" (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B 82B" --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 33 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 33 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.061A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 717 through 724 removed outlier: 7.024A pdb=" N MET G 757 " --> pdb=" O VAL L 718 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER L 720 " --> pdb=" O MET G 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA L 737 " --> pdb=" O LEU L 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU L 729 " --> pdb=" O ALA L 737 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.514A pdb=" N VAL H 16 " --> pdb=" O ARG H 82B" (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG H 82B" --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA H 33 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA H 33 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 7.060A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.687A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.340A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'J' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 180 " --> pdb=" O THR J 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR J 242 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA J 182 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET J 240 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR J 184 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 186 " --> pdb=" O ASN J 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN J 236 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU J 188 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU J 234 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.582A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY J 675 " --> pdb=" O PRO J 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 374 through 375 Processing sheet with id=AE8, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.313A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.560A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.471A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 617 through 619 removed outlier: 6.100A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AF4, first strand: chain 'K' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 83 through 85 removed outlier: 3.687A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.341A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AF8, first strand: chain 'K' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU K 180 " --> pdb=" O THR K 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR K 242 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA K 182 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET K 240 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR K 184 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 186 " --> pdb=" O ASN K 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN K 236 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU K 188 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU K 234 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG2, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.581A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY K 675 " --> pdb=" O PRO K 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS K 713 " --> pdb=" O PHE K 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG4, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.313A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.562A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR K 483 " --> pdb=" O VAL K 420 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL K 420 " --> pdb=" O THR K 483 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.472A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 617 through 619 removed outlier: 6.100A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AG9, first strand: chain 'L' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 83 through 85 removed outlier: 3.686A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 88 through 89 removed outlier: 7.340A pdb=" N SER L 88 " --> pdb=" O ILE L 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH4, first strand: chain 'L' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU L 180 " --> pdb=" O THR L 242 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR L 242 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA L 182 " --> pdb=" O MET L 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET L 240 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR L 184 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 186 " --> pdb=" O ASN L 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN L 236 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU L 188 " --> pdb=" O LEU L 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU L 234 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.583A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY L 675 " --> pdb=" O PRO L 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS L 713 " --> pdb=" O PHE L 674 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 374 through 375 Processing sheet with id=AH9, first strand: chain 'L' and resid 381 through 382 removed outlier: 6.312A pdb=" N VAL L 381 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS L 407 " --> pdb=" O CYS L 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'L' and resid 400 through 404 removed outlier: 3.561A pdb=" N LYS L 400 " --> pdb=" O TYR L 445 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR L 483 " --> pdb=" O VAL L 420 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL L 420 " --> pdb=" O THR L 483 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.471A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 617 through 619 removed outlier: 6.101A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3534 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: 9.60 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 5445 1.30 - 1.43: 9453 1.43 - 1.57: 18588 1.57 - 1.70: 3 1.70 - 1.84: 246 Bond restraints: 33735 Sorted by residual: bond pdb=" CA ASN K 236 " pdb=" C ASN K 236 " ideal model delta sigma weight residual 1.531 1.451 0.081 1.08e-02 8.57e+03 5.59e+01 bond pdb=" CA ASN L 236 " pdb=" C ASN L 236 " ideal model delta sigma weight residual 1.531 1.451 0.080 1.08e-02 8.57e+03 5.55e+01 bond pdb=" CA ASN J 236 " pdb=" C ASN J 236 " ideal model delta sigma weight residual 1.531 1.452 0.080 1.08e-02 8.57e+03 5.46e+01 bond pdb=" C CYS K 383 " pdb=" O CYS K 383 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.14e-02 7.69e+03 3.98e+01 bond pdb=" C CYS L 383 " pdb=" O CYS L 383 " ideal model delta sigma weight residual 1.234 1.162 0.071 1.14e-02 7.69e+03 3.90e+01 ... (remaining 33730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 41588 2.48 - 4.95: 3612 4.95 - 7.43: 527 7.43 - 9.90: 133 9.90 - 12.38: 16 Bond angle restraints: 45876 Sorted by residual: angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 120.21 129.96 -9.75 9.60e-01 1.09e+00 1.03e+02 angle pdb=" C VAL I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta sigma weight residual 120.21 129.92 -9.71 9.60e-01 1.09e+00 1.02e+02 angle pdb=" C VAL F 58 " pdb=" N PRO F 59 " pdb=" CA PRO F 59 " ideal model delta sigma weight residual 120.21 129.92 -9.71 9.60e-01 1.09e+00 1.02e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 126.82 -7.16 7.20e-01 1.93e+00 9.88e+01 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.80 -7.14 7.20e-01 1.93e+00 9.84e+01 ... (remaining 45871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 19016 17.24 - 34.47: 791 34.47 - 51.71: 192 51.71 - 68.94: 113 68.94 - 86.18: 27 Dihedral angle restraints: 20139 sinusoidal: 7749 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS A1106 " pdb=" SG CYS A1106 " pdb=" SG CYS A1117 " pdb=" CB CYS A1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.85 -82.85 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS G1106 " pdb=" SG CYS G1106 " pdb=" SG CYS G1117 " pdb=" CB CYS G1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.85 -82.85 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 20136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3437 0.075 - 0.150: 1440 0.150 - 0.225: 190 0.225 - 0.300: 18 0.300 - 0.375: 6 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CA CYS L 727 " pdb=" N CYS L 727 " pdb=" C CYS L 727 " pdb=" CB CYS L 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA CYS J 727 " pdb=" N CYS J 727 " pdb=" C CYS J 727 " pdb=" CB CYS J 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA CYS K 727 " pdb=" N CYS K 727 " pdb=" C CYS K 727 " pdb=" CB CYS K 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 5088 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO D1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO D1219 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO D1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO A1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO A1219 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO G1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO G1219 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO G1219 " 0.083 5.00e-02 4.00e+02 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 96 2.48 - 3.09: 25784 3.09 - 3.69: 51279 3.69 - 4.30: 80500 4.30 - 4.90: 123352 Nonbonded interactions: 281011 Sorted by model distance: nonbonded pdb=" CE2 PHE J 506 " pdb=" CG2 VAL J 555 " model vdw 1.881 3.760 nonbonded pdb=" CE1 PHE J 506 " pdb=" OE1 GLU J 513 " model vdw 1.882 3.340 nonbonded pdb=" CE1 PHE L 506 " pdb=" OE1 GLU L 513 " model vdw 1.883 3.340 nonbonded pdb=" CE1 PHE K 506 " pdb=" OE1 GLU K 513 " model vdw 1.883 3.340 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.928 3.760 ... (remaining 281006 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: 0.09 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.560 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.016 0.806 33792 Z= 0.959 Angle : 1.577 12.380 45990 Z= 1.049 Chirality : 0.075 0.375 5091 Planarity : 0.017 0.160 5961 Dihedral : 11.982 86.176 12066 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.21 % Allowed : 3.97 % Favored : 94.82 % Rotamer: Outliers : 0.90 % Allowed : 1.56 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 4227 helix: 0.52 (0.19), residues: 726 sheet: 0.02 (0.15), residues: 978 loop : 0.61 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 979 TYR 0.046 0.006 TYR L 438 PHE 0.035 0.004 PHE F 71 TRP 0.039 0.007 TRP G1184 HIS 0.009 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.01349 / 0.87 (33735) covalent geometry : angle 1.56938 / 1.05 (45876) SS BOND : bond 0.20103 / 13.42 ( 57) SS BOND : angle 3.57043 / 2.41 ( 114) hydrogen bonds : bond 0.15960 / 10.63 ( 1244) hydrogen bonds : angle 8.99853 / 6.33 ( 3534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: D 796 GLN cc_start: 0.9076 (tt0) cc_final: 0.8649 (tm-30) REVERT: D 906 MET cc_start: 0.2203 (ttt) cc_final: 0.1996 (mmt) REVERT: D 909 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.3673 (p90) REVERT: D 1012 PHE cc_start: 0.8741 (m-80) cc_final: 0.8509 (m-10) REVERT: D 1134 LEU cc_start: 0.9306 (mt) cc_final: 0.8750 (pt) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.0676 time to fit residues: 5.1800 Evaluate side-chains 24 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.135 Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0822 time to fit residues: 1.9517 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.037 Evaluate side-chains 33 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLU cc_start: 0.7827 (tp30) cc_final: 0.7278 (mp0) REVERT: F 70 ASP cc_start: 0.8380 (t0) cc_final: 0.7727 (m-30) REVERT: F 90 GLN cc_start: 0.8292 (tp40) cc_final: 0.7825 (pp30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0651 time to fit residues: 2.3162 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.033 Evaluate side-chains 81 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: J 169 LEU cc_start: 0.9112 (tp) cc_final: 0.8822 (tp) REVERT: J 218 ASN cc_start: 0.8593 (t0) cc_final: 0.7916 (p0) REVERT: J 277 ASN cc_start: 0.9161 (m110) cc_final: 0.8750 (m110) REVERT: J 288 ASP cc_start: 0.7579 (m-30) cc_final: 0.6859 (t0) REVERT: J 511 ARG cc_start: 0.3261 (mtm-85) cc_final: 0.2770 (ttt180) REVERT: J 593 ASP cc_start: 0.6622 (t0) cc_final: 0.6349 (m-30) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.0745 time to fit residues: 8.1159 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.0050 chunk 388 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 0.1980 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 0.7980 overall best weight: 0.0636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 76 HIS ** J 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050329 restraints weight = 24315.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051571 restraints weight = 15374.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052435 restraints weight = 10846.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053031 restraints weight = 8297.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053412 restraints weight = 6755.623| |-----------------------------------------------------------------------------| r_work (final): 0.3110 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.045780 restraints weight = 9283.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046877 restraints weight = 6169.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047677 restraints weight = 4433.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048275 restraints weight = 3337.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048718 restraints weight = 2617.845| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050671 restraints weight = 7953.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051775 restraints weight = 5648.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052572 restraints weight = 4265.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053118 restraints weight = 3419.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053499 restraints weight = 2856.424| |-----------------------------------------------------------------------------| r_work (final): 0.3396 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.056988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.046561 restraints weight = 64293.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.047541 restraints weight = 42983.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.048260 restraints weight = 31402.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.048765 restraints weight = 24843.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049098 restraints weight = 20828.498| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33792 Z= 0.158 Angle : 0.717 8.554 45990 Z= 0.394 Chirality : 0.045 0.186 5091 Planarity : 0.008 0.094 5961 Dihedral : 5.930 36.896 4629 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.26 % Favored : 95.24 % Rotamer: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4227 helix: 0.90 (0.19), residues: 696 sheet: 0.14 (0.15), residues: 1023 loop : 0.10 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 181 TYR 0.020 0.002 TYR D1141 PHE 0.023 0.002 PHE C 87 TRP 0.030 0.002 TRP B 47 HIS 0.006 0.001 HIS K 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (33735) covalent geometry : angle 0.70922 / 0.39 (45876) SS BOND : bond 0.00568 / 0.36 ( 57) SS BOND : angle 2.17055 / 1.41 ( 114) hydrogen bonds : bond 0.05452 / 3.66 ( 1244) hydrogen bonds : angle 6.89659 / 4.87 ( 3534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 796 GLN cc_start: 0.9037 (tt0) cc_final: 0.8726 (tm-30) REVERT: D 925 CYS cc_start: 0.1274 (OUTLIER) cc_final: 0.0968 (p) REVERT: D 928 TYR cc_start: 0.6203 (p90) cc_final: 0.5920 (t80) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0465 time to fit residues: 3.1320 Evaluate side-chains 27 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.138 Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8551 (m-40) cc_final: 0.8339 (m110) REVERT: E 69 MET cc_start: 0.6772 (tpt) cc_final: 0.6534 (mmm) REVERT: E 105 GLN cc_start: 0.8220 (pm20) cc_final: 0.7905 (pm20) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0880 time to fit residues: 1.9920 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.037 Evaluate side-chains 25 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 70 ASP cc_start: 0.8110 (t0) cc_final: 0.7393 (m-30) REVERT: F 90 GLN cc_start: 0.7631 (tp40) cc_final: 0.7008 (pp30) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0666 time to fit residues: 1.8093 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.037 Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: K 116 PHE cc_start: 0.7822 (p90) cc_final: 0.7408 (p90) REVERT: K 288 ASP cc_start: 0.7441 (m-30) cc_final: 0.6977 (t0) REVERT: K 452 MET cc_start: 0.4176 (ttm) cc_final: 0.3774 (ptm) REVERT: K 511 ARG cc_start: 0.3068 (mtm-85) cc_final: 0.2596 (ttt180) REVERT: K 611 VAL cc_start: 0.9145 (p) cc_final: 0.8938 (m) REVERT: K 638 LEU cc_start: 0.8846 (tp) cc_final: 0.8611 (tp) REVERT: K 696 MET cc_start: 0.5578 (pmm) cc_final: 0.5326 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0654 time to fit residues: 5.3559 Evaluate side-chains 39 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 272 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 251 optimal weight: 0.2980 chunk 405 optimal weight: 0.0570 chunk 211 optimal weight: 7.9990 chunk 392 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1097 GLN K 637 ASN K 733 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049199 restraints weight = 23856.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050531 restraints weight = 15089.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051380 restraints weight = 10661.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052069 restraints weight = 8244.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052631 restraints weight = 6700.989| |-----------------------------------------------------------------------------| r_work (final): 0.3090 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.049618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043484 restraints weight = 10597.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.044657 restraints weight = 6439.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045488 restraints weight = 4379.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046117 restraints weight = 3240.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046561 restraints weight = 2513.268| |-----------------------------------------------------------------------------| r_work (final): 0.3212 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.060717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.053838 restraints weight = 7900.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054974 restraints weight = 5655.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.055706 restraints weight = 4348.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.056260 restraints weight = 3514.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.056698 restraints weight = 2949.345| |-----------------------------------------------------------------------------| r_work (final): 0.3423 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.056641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.046511 restraints weight = 68009.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.047457 restraints weight = 44215.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.048165 restraints weight = 32107.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.048678 restraints weight = 25173.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048955 restraints weight = 20973.691| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33792 Z= 0.128 Angle : 0.648 7.885 45990 Z= 0.350 Chirality : 0.044 0.202 5091 Planarity : 0.006 0.075 5961 Dihedral : 5.451 32.865 4629 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.26 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4227 helix: 1.09 (0.19), residues: 693 sheet: 0.20 (0.15), residues: 1050 loop : 0.12 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.031 0.001 TYR I 28 PHE 0.023 0.002 PHE I 87 TRP 0.022 0.002 TRP H 103 HIS 0.005 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (33735) covalent geometry : angle 0.63952 / 0.35 (45876) SS BOND : bond 0.00258 / 0.15 ( 57) SS BOND : angle 2.17008 / 1.38 ( 114) hydrogen bonds : bond 0.04721 / 3.18 ( 1244) hydrogen bonds : angle 6.31470 / 4.48 ( 3534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0413 time to fit residues: 1.8099 Evaluate side-chains 18 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.135 Evaluate side-chains 17 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 69 MET cc_start: 0.6409 (tpt) cc_final: 0.5917 (mmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0769 time to fit residues: 1.4388 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.038 Evaluate side-chains 22 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: I 70 ASP cc_start: 0.8466 (t0) cc_final: 0.7891 (m-30) REVERT: I 73 LEU cc_start: 0.8612 (tp) cc_final: 0.8321 (tp) REVERT: I 85 MET cc_start: 0.7440 (tpt) cc_final: 0.5366 (tpt) REVERT: I 86 TYR cc_start: 0.7747 (m-80) cc_final: 0.7506 (m-10) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0687 time to fit residues: 1.6504 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.050 Evaluate side-chains 52 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: K 218 ASN cc_start: 0.7741 (t0) cc_final: 0.7111 (m110) REVERT: K 288 ASP cc_start: 0.7351 (m-30) cc_final: 0.6844 (t0) REVERT: K 289 THR cc_start: 0.7586 (m) cc_final: 0.6716 (p) REVERT: K 452 MET cc_start: 0.4370 (ttm) cc_final: 0.4158 (ptm) REVERT: K 511 ARG cc_start: 0.3124 (mtm-85) cc_final: 0.2588 (ttt180) REVERT: K 638 LEU cc_start: 0.8791 (tp) cc_final: 0.8560 (tp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0630 time to fit residues: 4.7306 Evaluate side-chains 40 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 414 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 0.1980 chunk 217 optimal weight: 7.9990 chunk 248 optimal weight: 40.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 HIS D1163 ASN E 3 GLN K 377 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047748 restraints weight = 24570.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049081 restraints weight = 15433.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049989 restraints weight = 10883.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050543 restraints weight = 8332.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051104 restraints weight = 6927.786| |-----------------------------------------------------------------------------| r_work (final): 0.3049 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042811 restraints weight = 10644.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.043868 restraints weight = 6209.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044556 restraints weight = 4039.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045018 restraints weight = 2882.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045351 restraints weight = 2211.064| |-----------------------------------------------------------------------------| r_work (final): 0.3108 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.059116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052818 restraints weight = 6862.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.053831 restraints weight = 4881.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.054602 restraints weight = 3744.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.055135 restraints weight = 3024.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.055611 restraints weight = 2549.979| |-----------------------------------------------------------------------------| r_work (final): 0.3447 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.055187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.045274 restraints weight = 68267.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.046198 restraints weight = 44705.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.046857 restraints weight = 32539.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047320 restraints weight = 25582.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.047637 restraints weight = 21355.879| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33792 Z= 0.140 Angle : 0.630 10.410 45990 Z= 0.336 Chirality : 0.043 0.161 5091 Planarity : 0.005 0.070 5961 Dihedral : 5.275 33.697 4629 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.68 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4227 helix: 1.39 (0.20), residues: 678 sheet: 0.18 (0.15), residues: 1062 loop : -0.08 (0.13), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 94 TYR 0.020 0.001 TYR G 909 PHE 0.030 0.002 PHE C 87 TRP 0.017 0.002 TRP H 103 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (33735) covalent geometry : angle 0.61972 / 0.33 (45876) SS BOND : bond 0.00738 / 0.52 ( 57) SS BOND : angle 2.33340 / 1.53 ( 114) hydrogen bonds : bond 0.04267 / 2.88 ( 1244) hydrogen bonds : angle 6.04092 / 4.29 ( 3534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 927 GLN cc_start: 0.7430 (mt0) cc_final: 0.6024 (pp30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0514 time to fit residues: 2.1918 Evaluate side-chains 24 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.149 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 ASN cc_start: 0.8646 (m110) cc_final: 0.8290 (p0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0893 time to fit residues: 1.5586 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.037 Evaluate side-chains 18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLU cc_start: 0.8042 (pp20) cc_final: 0.7724 (pm20) REVERT: F 70 ASP cc_start: 0.7838 (t0) cc_final: 0.7456 (m-30) REVERT: F 73 LEU cc_start: 0.8358 (tp) cc_final: 0.8151 (tp) REVERT: F 85 MET cc_start: 0.7474 (tpt) cc_final: 0.6892 (tpt) REVERT: F 86 TYR cc_start: 0.7767 (m-80) cc_final: 0.7475 (m-10) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0580 time to fit residues: 1.1570 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 Evaluate side-chains 43 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8387 (m-10) cc_final: 0.8107 (m-80) REVERT: K 218 ASN cc_start: 0.7909 (t0) cc_final: 0.7267 (m110) REVERT: K 225 LEU cc_start: 0.8957 (tp) cc_final: 0.8618 (mt) REVERT: K 288 ASP cc_start: 0.7453 (m-30) cc_final: 0.6900 (t0) REVERT: K 289 THR cc_start: 0.7667 (m) cc_final: 0.6807 (p) REVERT: K 452 MET cc_start: 0.4587 (ttm) cc_final: 0.4320 (ptm) REVERT: K 511 ARG cc_start: 0.3245 (mtm-85) cc_final: 0.2710 (ttt180) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0564 time to fit residues: 3.6381 Evaluate side-chains 37 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 304 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 372 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 0.0570 chunk 184 optimal weight: 0.0970 chunk 100 optimal weight: 0.0870 chunk 206 optimal weight: 10.0000 overall best weight: 1.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 836 HIS ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048809 restraints weight = 24274.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049957 restraints weight = 15395.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.050910 restraints weight = 11324.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051653 restraints weight = 8667.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052088 restraints weight = 7011.882| |-----------------------------------------------------------------------------| r_work (final): 0.3072 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.049064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.044407 restraints weight = 10304.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.045479 restraints weight = 6314.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046182 restraints weight = 4272.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046681 restraints weight = 3128.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047072 restraints weight = 2442.595| |-----------------------------------------------------------------------------| r_work (final): 0.3218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.059788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052735 restraints weight = 7514.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.053888 restraints weight = 5119.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.054797 restraints weight = 3861.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055447 restraints weight = 3068.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.055961 restraints weight = 2542.547| |-----------------------------------------------------------------------------| r_work (final): 0.3454 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.055605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.045512 restraints weight = 67414.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046459 restraints weight = 44866.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047119 restraints weight = 32936.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.047583 restraints weight = 26015.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.047887 restraints weight = 21728.754| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33792 Z= 0.113 Angle : 0.624 9.889 45990 Z= 0.329 Chirality : 0.043 0.155 5091 Planarity : 0.005 0.060 5961 Dihedral : 5.102 33.733 4629 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.05 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4227 helix: 1.60 (0.20), residues: 678 sheet: 0.42 (0.17), residues: 933 loop : -0.21 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 652 TYR 0.024 0.001 TYR I 28 PHE 0.020 0.001 PHE I 87 TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS G1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (33735) covalent geometry : angle 0.61074 / 0.32 (45876) SS BOND : bond 0.00307 / 0.20 ( 57) SS BOND : angle 2.63932 / 1.69 ( 114) hydrogen bonds : bond 0.03979 / 2.68 ( 1244) hydrogen bonds : angle 5.75303 / 4.08 ( 3534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: D 927 GLN cc_start: 0.7410 (mt0) cc_final: 0.6034 (pp30) REVERT: D 1134 LEU cc_start: 0.9320 (mt) cc_final: 0.9070 (mt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0417 time to fit residues: 1.8864 Evaluate side-chains 23 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.128 Evaluate side-chains 14 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0669 time to fit residues: 1.0508 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.038 Evaluate side-chains 18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: F 15 LEU cc_start: 0.6981 (mp) cc_final: 0.6634 (mt) REVERT: F 27 GLU cc_start: 0.7867 (pp20) cc_final: 0.7520 (pm20) REVERT: F 70 ASP cc_start: 0.8163 (t0) cc_final: 0.7694 (m-30) REVERT: F 73 LEU cc_start: 0.8694 (tp) cc_final: 0.8328 (tp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0601 time to fit residues: 1.1996 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8359 (m-10) cc_final: 0.8046 (m-80) REVERT: K 218 ASN cc_start: 0.7786 (t0) cc_final: 0.7272 (m110) REVERT: K 225 LEU cc_start: 0.8956 (tp) cc_final: 0.8635 (mt) REVERT: K 288 ASP cc_start: 0.7369 (m-30) cc_final: 0.6797 (t0) REVERT: K 289 THR cc_start: 0.7673 (m) cc_final: 0.6806 (p) REVERT: K 324 LEU cc_start: 0.8462 (tp) cc_final: 0.8217 (tt) REVERT: K 511 ARG cc_start: 0.3245 (mtm-85) cc_final: 0.2715 (ttt180) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0664 time to fit residues: 4.2722 Evaluate side-chains 35 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 345 optimal weight: 0.0470 chunk 249 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 330 optimal weight: 20.0000 chunk 194 optimal weight: 0.0970 chunk 196 optimal weight: 3.9990 chunk 364 optimal weight: 7.9990 chunk 306 optimal weight: 0.2980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 836 HIS ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049694 restraints weight = 23842.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.050849 restraints weight = 15573.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051676 restraints weight = 11180.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052374 restraints weight = 8650.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052848 restraints weight = 6988.907| |-----------------------------------------------------------------------------| r_work (final): 0.3104 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.048576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043565 restraints weight = 10433.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.044547 restraints weight = 6678.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045264 restraints weight = 4704.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.045789 restraints weight = 3536.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046176 restraints weight = 2794.848| |-----------------------------------------------------------------------------| r_work (final): 0.3205 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.059373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052823 restraints weight = 6513.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053964 restraints weight = 4493.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.054853 restraints weight = 3325.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.055469 restraints weight = 2611.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.055954 restraints weight = 2171.075| |-----------------------------------------------------------------------------| r_work (final): 0.3442 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.056066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.045897 restraints weight = 65959.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.046811 restraints weight = 43875.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.047480 restraints weight = 32282.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.047898 restraints weight = 25458.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.048216 restraints weight = 21497.071| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33792 Z= 0.108 Angle : 0.600 8.322 45990 Z= 0.315 Chirality : 0.043 0.220 5091 Planarity : 0.005 0.056 5961 Dihedral : 4.882 34.566 4629 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.47 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4227 helix: 1.91 (0.20), residues: 663 sheet: 0.30 (0.16), residues: 1005 loop : -0.21 (0.13), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 758 TYR 0.017 0.001 TYR K 438 PHE 0.040 0.001 PHE A 977 TRP 0.011 0.001 TRP B 103 HIS 0.003 0.001 HIS G1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (33735) covalent geometry : angle 0.58925 / 0.31 (45876) SS BOND : bond 0.00271 / 0.16 ( 57) SS BOND : angle 2.32737 / 1.52 ( 114) hydrogen bonds : bond 0.03803 / 2.57 ( 1244) hydrogen bonds : angle 5.41085 / 3.86 ( 3534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 927 GLN cc_start: 0.7396 (mt0) cc_final: 0.5935 (pp30) REVERT: D 935 LEU cc_start: 0.9332 (mt) cc_final: 0.8903 (tt) REVERT: D 1134 LEU cc_start: 0.9330 (mt) cc_final: 0.9081 (mt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0393 time to fit residues: 1.8808 Evaluate side-chains 22 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.151 Evaluate side-chains 14 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.038 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1023 time to fit residues: 1.5470 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.038 Evaluate side-chains 18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: F 15 LEU cc_start: 0.7192 (mp) cc_final: 0.6908 (mt) REVERT: F 27 GLU cc_start: 0.8352 (pp20) cc_final: 0.8036 (pm20) REVERT: F 70 ASP cc_start: 0.8018 (t0) cc_final: 0.7580 (m-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1008 time to fit residues: 1.9358 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.034 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8195 (m-10) cc_final: 0.7860 (m-80) REVERT: K 218 ASN cc_start: 0.7674 (t0) cc_final: 0.7311 (m110) REVERT: K 225 LEU cc_start: 0.8852 (tp) cc_final: 0.8555 (mt) REVERT: K 288 ASP cc_start: 0.7377 (m-30) cc_final: 0.6748 (t0) REVERT: K 289 THR cc_start: 0.7651 (m) cc_final: 0.6757 (p) REVERT: K 511 ARG cc_start: 0.3398 (mtm-85) cc_final: 0.2838 (ttt180) REVERT: K 717 LEU cc_start: 0.7418 (mt) cc_final: 0.7062 (tp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0637 time to fit residues: 4.1386 Evaluate side-chains 32 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 342 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 15 optimal weight: 0.0370 chunk 366 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 overall best weight: 2.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 836 HIS ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.055020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047152 restraints weight = 25971.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048281 restraints weight = 16741.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049099 restraints weight = 12019.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049693 restraints weight = 9296.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050162 restraints weight = 7606.802| |-----------------------------------------------------------------------------| r_work (final): 0.3073 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.047340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041826 restraints weight = 10231.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.042726 restraints weight = 6777.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.043438 restraints weight = 4931.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043954 restraints weight = 3808.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044348 restraints weight = 3091.916| |-----------------------------------------------------------------------------| r_work (final): 0.3140 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.051931 restraints weight = 7104.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052858 restraints weight = 5188.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053716 restraints weight = 4090.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.054363 restraints weight = 3326.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.054809 restraints weight = 2758.649| |-----------------------------------------------------------------------------| r_work (final): 0.3389 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.055339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045188 restraints weight = 67332.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.046099 restraints weight = 44355.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.046732 restraints weight = 32576.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.047227 restraints weight = 25781.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.047522 restraints weight = 21423.983| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33792 Z= 0.115 Angle : 0.616 9.869 45990 Z= 0.321 Chirality : 0.042 0.199 5091 Planarity : 0.005 0.057 5961 Dihedral : 4.879 34.357 4629 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.54 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4227 helix: 1.73 (0.20), residues: 684 sheet: 0.25 (0.16), residues: 1014 loop : -0.24 (0.13), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 758 TYR 0.018 0.001 TYR K 438 PHE 0.023 0.002 PHE A 977 TRP 0.018 0.002 TRP B 47 HIS 0.005 0.001 HIS D1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (33735) covalent geometry : angle 0.60172 / 0.32 (45876) SS BOND : bond 0.00256 / 0.15 ( 57) SS BOND : angle 2.68696 / 1.71 ( 114) hydrogen bonds : bond 0.03697 / 2.49 ( 1244) hydrogen bonds : angle 5.42746 / 3.85 ( 3534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 927 GLN cc_start: 0.7209 (mt0) cc_final: 0.5526 (pp30) REVERT: A 935 LEU cc_start: 0.9371 (mt) cc_final: 0.9081 (mp) REVERT: A 1134 LEU cc_start: 0.9355 (mt) cc_final: 0.9145 (mm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0398 time to fit residues: 1.8328 Evaluate side-chains 21 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.139 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.039 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0553 time to fit residues: 0.7723 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.037 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: F 15 LEU cc_start: 0.6882 (mp) cc_final: 0.6602 (mt) REVERT: F 70 ASP cc_start: 0.7942 (t0) cc_final: 0.7524 (m-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0566 time to fit residues: 0.9651 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Evaluate side-chains 41 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8266 (m-10) cc_final: 0.7988 (m-80) REVERT: K 218 ASN cc_start: 0.7711 (t0) cc_final: 0.7366 (m110) REVERT: K 225 LEU cc_start: 0.8867 (tp) cc_final: 0.8564 (mt) REVERT: K 278 MET cc_start: 0.7403 (tpt) cc_final: 0.6841 (tpp) REVERT: K 288 ASP cc_start: 0.7396 (m-30) cc_final: 0.6771 (t0) REVERT: K 289 THR cc_start: 0.7672 (m) cc_final: 0.6818 (p) REVERT: K 511 ARG cc_start: 0.3573 (mtm-85) cc_final: 0.2987 (ttt180) REVERT: K 639 VAL cc_start: 0.8599 (m) cc_final: 0.8311 (p) REVERT: K 686 MET cc_start: 0.7444 (mmt) cc_final: 0.6963 (mmt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0672 time to fit residues: 4.0489 Evaluate side-chains 33 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 313 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 346 optimal weight: 0.0170 chunk 288 optimal weight: 4.9990 chunk 398 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 325 optimal weight: 30.0000 chunk 224 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 HIS ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN K 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.057534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049183 restraints weight = 23972.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050421 restraints weight = 15374.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051276 restraints weight = 10899.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051784 restraints weight = 8302.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052270 restraints weight = 6840.508| |-----------------------------------------------------------------------------| r_work (final): 0.3098 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041826 restraints weight = 10230.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042743 restraints weight = 6697.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043451 restraints weight = 4813.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.043969 restraints weight = 3684.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044352 restraints weight = 2983.853| |-----------------------------------------------------------------------------| r_work (final): 0.3131 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.058392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052061 restraints weight = 7295.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052605 restraints weight = 5924.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.053251 restraints weight = 5057.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.053701 restraints weight = 4341.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.054205 restraints weight = 3816.654| |-----------------------------------------------------------------------------| r_work (final): 0.3373 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.055630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045423 restraints weight = 67271.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.046339 restraints weight = 44608.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.046989 restraints weight = 32910.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.047455 restraints weight = 26132.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.047744 restraints weight = 21894.170| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33792 Z= 0.102 Angle : 0.592 8.730 45990 Z= 0.310 Chirality : 0.042 0.181 5091 Planarity : 0.004 0.056 5961 Dihedral : 4.755 34.621 4629 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4227 helix: 1.92 (0.20), residues: 669 sheet: 0.25 (0.16), residues: 1014 loop : -0.24 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 119 TYR 0.016 0.001 TYR K 438 PHE 0.021 0.001 PHE G 977 TRP 0.028 0.002 TRP H 103 HIS 0.003 0.001 HIS G 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (33735) covalent geometry : angle 0.58058 / 0.30 (45876) SS BOND : bond 0.00238 / 0.14 ( 57) SS BOND : angle 2.40228 / 1.54 ( 114) hydrogen bonds : bond 0.03537 / 2.39 ( 1244) hydrogen bonds : angle 5.26773 / 3.75 ( 3534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 927 GLN cc_start: 0.7318 (mt0) cc_final: 0.5663 (pp30) REVERT: D 935 LEU cc_start: 0.9289 (mt) cc_final: 0.9020 (mp) REVERT: D 1134 LEU cc_start: 0.9255 (mt) cc_final: 0.9041 (mt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0401 time to fit residues: 1.7952 Evaluate side-chains 22 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.136 Evaluate side-chains 15 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: E 27 TYR cc_start: 0.5788 (p90) cc_final: 0.5353 (p90) REVERT: E 69 MET cc_start: 0.6996 (mmm) cc_final: 0.6460 (mmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0630 time to fit residues: 1.0615 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: F 1 ASP cc_start: 0.7595 (p0) cc_final: 0.6990 (p0) REVERT: F 15 LEU cc_start: 0.7085 (mp) cc_final: 0.6748 (mt) REVERT: F 27 GLU cc_start: 0.8571 (pm20) cc_final: 0.8160 (pm20) REVERT: F 70 ASP cc_start: 0.7955 (t0) cc_final: 0.7572 (m-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0537 time to fit residues: 0.9093 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.033 Evaluate side-chains 40 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.231 Fit side-chains REVERT: K 147 PHE cc_start: 0.8233 (m-10) cc_final: 0.7944 (m-80) REVERT: K 218 ASN cc_start: 0.7800 (t0) cc_final: 0.7443 (m110) REVERT: K 225 LEU cc_start: 0.8942 (tp) cc_final: 0.8656 (mt) REVERT: K 278 MET cc_start: 0.8355 (tpp) cc_final: 0.7830 (tpp) REVERT: K 288 ASP cc_start: 0.7335 (m-30) cc_final: 0.6681 (t0) REVERT: K 289 THR cc_start: 0.7650 (m) cc_final: 0.6771 (p) REVERT: K 511 ARG cc_start: 0.3572 (mtm-85) cc_final: 0.3019 (ttt180) REVERT: K 639 VAL cc_start: 0.8615 (m) cc_final: 0.8365 (p) REVERT: K 686 MET cc_start: 0.7332 (mmt) cc_final: 0.6787 (mmt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0620 time to fit residues: 3.7031 Evaluate side-chains 32 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 205 optimal weight: 3.9990 chunk 376 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 45 optimal weight: 0.0870 chunk 120 optimal weight: 0.0170 chunk 246 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046749 restraints weight = 26277.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047879 restraints weight = 16857.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048728 restraints weight = 12073.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049361 restraints weight = 9244.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049887 restraints weight = 7478.573| |-----------------------------------------------------------------------------| r_work (final): 0.3071 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.046235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041181 restraints weight = 10024.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.042111 restraints weight = 6553.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042760 restraints weight = 4723.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.043239 restraints weight = 3622.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043618 restraints weight = 2946.926| |-----------------------------------------------------------------------------| r_work (final): 0.3108 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.058554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051220 restraints weight = 6945.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051933 restraints weight = 5340.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052563 restraints weight = 4409.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053090 restraints weight = 3804.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.053490 restraints weight = 3350.201| |-----------------------------------------------------------------------------| r_work (final): 0.3368 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.055572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045445 restraints weight = 66697.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.046370 restraints weight = 44451.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047021 restraints weight = 32321.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.047394 restraints weight = 25547.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.047773 restraints weight = 21745.413| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33792 Z= 0.111 Angle : 0.606 8.564 45990 Z= 0.318 Chirality : 0.043 0.211 5091 Planarity : 0.004 0.053 5961 Dihedral : 4.729 33.257 4629 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4227 helix: 1.99 (0.20), residues: 669 sheet: 0.12 (0.16), residues: 1032 loop : -0.23 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.016 0.001 TYR K 438 PHE 0.058 0.002 PHE C 36 TRP 0.047 0.002 TRP B 103 HIS 0.005 0.001 HIS D1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (33735) covalent geometry : angle 0.59629 / 0.31 (45876) SS BOND : bond 0.00234 / 0.14 ( 57) SS BOND : angle 2.26315 / 1.46 ( 114) hydrogen bonds : bond 0.03524 / 2.38 ( 1244) hydrogen bonds : angle 5.29982 / 3.78 ( 3534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 LEU cc_start: 0.9372 (mt) cc_final: 0.9109 (mp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0384 time to fit residues: 1.7286 Evaluate side-chains 20 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.144 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: E 69 MET cc_start: 0.6984 (mmm) cc_final: 0.6449 (mmm) REVERT: E 100 MET cc_start: 0.7551 (tpp) cc_final: 0.7179 (tpt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0549 time to fit residues: 0.7046 Evaluate side-chains 8 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.040 Evaluate side-chains 18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: F 1 ASP cc_start: 0.7798 (p0) cc_final: 0.7212 (p0) REVERT: F 15 LEU cc_start: 0.7224 (mp) cc_final: 0.6863 (mt) REVERT: F 27 GLU cc_start: 0.8602 (pm20) cc_final: 0.8005 (pm20) REVERT: F 36 PHE cc_start: 0.7908 (m-80) cc_final: 0.6964 (m-80) REVERT: F 70 ASP cc_start: 0.7985 (t0) cc_final: 0.7543 (m-30) REVERT: F 73 LEU cc_start: 0.8590 (tp) cc_final: 0.8278 (tp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0747 time to fit residues: 1.4636 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.034 Evaluate side-chains 41 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.243 Fit side-chains REVERT: K 218 ASN cc_start: 0.7758 (t0) cc_final: 0.7470 (m110) REVERT: K 225 LEU cc_start: 0.8978 (tp) cc_final: 0.8688 (mt) REVERT: K 278 MET cc_start: 0.8396 (tpp) cc_final: 0.7783 (tpp) REVERT: K 288 ASP cc_start: 0.7314 (m-30) cc_final: 0.6701 (t0) REVERT: K 289 THR cc_start: 0.7643 (m) cc_final: 0.6779 (m) REVERT: K 511 ARG cc_start: 0.3679 (mtm-85) cc_final: 0.3138 (ttt180) REVERT: K 639 VAL cc_start: 0.8642 (m) cc_final: 0.8412 (p) REVERT: K 686 MET cc_start: 0.7510 (mmt) cc_final: 0.7073 (mmt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0805 time to fit residues: 4.5473 Evaluate side-chains 32 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 150 optimal weight: 7.9990 chunk 201 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 408 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 239 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN K 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.053992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046078 restraints weight = 27076.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047283 restraints weight = 16730.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048105 restraints weight = 11640.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048731 restraints weight = 8824.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049153 restraints weight = 7083.673| |-----------------------------------------------------------------------------| r_work (final): 0.3055 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.046480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042223 restraints weight = 10117.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043253 restraints weight = 5878.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043969 restraints weight = 3809.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044467 restraints weight = 2677.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044831 restraints weight = 2001.686| |-----------------------------------------------------------------------------| r_work (final): 0.3117 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.057205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048837 restraints weight = 6698.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049788 restraints weight = 4913.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050456 restraints weight = 3945.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051013 restraints weight = 3382.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.051434 restraints weight = 2976.578| |-----------------------------------------------------------------------------| r_work (final): 0.3320 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.054879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.044808 restraints weight = 68390.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045694 restraints weight = 45805.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.046315 restraints weight = 33774.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.046752 restraints weight = 26836.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.047061 restraints weight = 22558.200| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33792 Z= 0.125 Angle : 0.623 8.961 45990 Z= 0.328 Chirality : 0.043 0.202 5091 Planarity : 0.005 0.059 5961 Dihedral : 4.777 35.019 4629 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4227 helix: 1.83 (0.20), residues: 669 sheet: 0.26 (0.16), residues: 1014 loop : -0.37 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 758 TYR 0.019 0.001 TYR J 448 PHE 0.026 0.002 PHE A 977 TRP 0.038 0.002 TRP B 103 HIS 0.003 0.001 HIS J 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (33735) covalent geometry : angle 0.61371 / 0.32 (45876) SS BOND : bond 0.00238 / 0.15 ( 57) SS BOND : angle 2.23112 / 1.44 ( 114) hydrogen bonds : bond 0.03630 / 2.43 ( 1244) hydrogen bonds : angle 5.22519 / 3.74 ( 3534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 874 LEU cc_start: 0.8904 (mt) cc_final: 0.8434 (pt) REVERT: A 927 GLN cc_start: 0.7487 (mt0) cc_final: 0.5426 (pp30) REVERT: A 935 LEU cc_start: 0.9363 (mt) cc_final: 0.9072 (mp) REVERT: A 1134 LEU cc_start: 0.9275 (mm) cc_final: 0.9052 (mt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0365 time to fit residues: 1.5536 Evaluate side-chains 20 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.141 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: B 100 MET cc_start: 0.7562 (tpp) cc_final: 0.7257 (tpp) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0536 time to fit residues: 0.6900 Evaluate side-chains 8 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.041 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.035 Fit side-chains REVERT: F 1 ASP cc_start: 0.7773 (p0) cc_final: 0.7187 (p0) REVERT: F 15 LEU cc_start: 0.6857 (mp) cc_final: 0.6490 (mt) REVERT: F 27 GLU cc_start: 0.8648 (pm20) cc_final: 0.8227 (pm20) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0634 time to fit residues: 0.9911 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.036 Evaluate side-chains 40 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.223 Fit side-chains REVERT: K 147 PHE cc_start: 0.8230 (m-80) cc_final: 0.7908 (m-80) REVERT: K 218 ASN cc_start: 0.7876 (t0) cc_final: 0.7588 (m110) REVERT: K 225 LEU cc_start: 0.8983 (tp) cc_final: 0.8682 (mt) REVERT: K 278 MET cc_start: 0.8495 (tpp) cc_final: 0.8130 (tpp) REVERT: K 288 ASP cc_start: 0.7366 (m-30) cc_final: 0.6761 (t0) REVERT: K 289 THR cc_start: 0.7658 (m) cc_final: 0.6777 (m) REVERT: K 379 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6858 (mp0) REVERT: K 511 ARG cc_start: 0.3737 (mtm-85) cc_final: 0.3175 (ttt180) REVERT: K 686 MET cc_start: 0.7711 (mmt) cc_final: 0.7433 (mmt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0610 time to fit residues: 3.6466 Evaluate side-chains 30 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 302 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 HIS K 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045678 restraints weight = 26160.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046908 restraints weight = 16355.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047730 restraints weight = 11465.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048397 restraints weight = 8785.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048908 restraints weight = 7108.728| |-----------------------------------------------------------------------------| r_work (final): 0.3014 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.045361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041035 restraints weight = 10413.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042044 restraints weight = 6027.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042734 restraints weight = 3929.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.043204 restraints weight = 2785.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.043545 restraints weight = 2104.429| |-----------------------------------------------------------------------------| r_work (final): 0.3077 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050522 restraints weight = 7427.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051363 restraints weight = 5656.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.052007 restraints weight = 4665.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052467 restraints weight = 4015.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052500 restraints weight = 3605.422| |-----------------------------------------------------------------------------| r_work (final): 0.3350 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.053620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.043703 restraints weight = 68678.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.044590 restraints weight = 46233.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.045201 restraints weight = 34128.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.045671 restraints weight = 27088.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.045930 restraints weight = 22788.761| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33792 Z= 0.162 Angle : 0.650 9.901 45990 Z= 0.338 Chirality : 0.043 0.187 5091 Planarity : 0.005 0.059 5961 Dihedral : 4.966 34.815 4629 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 4227 helix: 1.26 (0.20), residues: 702 sheet: 0.29 (0.17), residues: 957 loop : -0.42 (0.13), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 758 TYR 0.019 0.002 TYR K 438 PHE 0.019 0.002 PHE C 36 TRP 0.034 0.002 TRP B 103 HIS 0.004 0.001 HIS J 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (33735) covalent geometry : angle 0.64076 / 0.33 (45876) SS BOND : bond 0.00260 / 0.17 ( 57) SS BOND : angle 2.25651 / 1.46 ( 114) hydrogen bonds : bond 0.03765 / 2.51 ( 1244) hydrogen bonds : angle 5.40801 / 3.87 ( 3534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.15 seconds wall clock time: 53 minutes 59.63 seconds (3239.63 seconds total)