Starting phenix.real_space_refine on Mon Aug 10 05:50:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmn_48395/08_2026/9mmn_48395.map" } resolution = 3.6 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= 0.009 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: 6 Type Number sf(0) Gaussians P 570 5.49 5 S 28 5.16 5 C 13060 2.51 5 N 4428 2.21 5 O 5526 1.98 5 H 18934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "N" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "R" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "X" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "Y" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 5.48, per 1000 atoms: 0.13 Number of scatterers: 42546 At special positions: 0 Unit cell: (126.28, 139.37, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 570 15.00 O 5526 8.00 N 4428 7.00 C 13060 6.00 H 18934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 682.9 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 20 sheets defined 72.2% alpha, 2.9% beta 282 base pairs and 524 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.547A pdb=" N GLN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.863A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.659A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.711A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.650A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 removed outlier: 4.007A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.863A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 removed outlier: 3.815A pdb=" N SER D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.569A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.556A pdb=" N GLN E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.863A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.669A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.141A pdb=" N ILE F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.837A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.640A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.511A pdb=" N ILE H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 67 " --> pdb=" O MET H 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.657A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 64 through 77 removed outlier: 3.546A pdb=" N GLN L 77 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 114 removed outlier: 3.863A pdb=" N VAL L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU L 110 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS L 111 " --> pdb=" O ASP L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 133 removed outlier: 3.659A pdb=" N ILE L 125 " --> pdb=" O MET L 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 31 through 42 Processing helix chain 'M' and resid 50 through 77 removed outlier: 3.711A pdb=" N GLU M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU M 64 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN M 65 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 94 removed outlier: 3.650A pdb=" N GLN M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 23 Processing helix chain 'N' and resid 27 through 38 Processing helix chain 'N' and resid 47 through 74 removed outlier: 4.007A pdb=" N LEU N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'N' and resid 93 through 98 Processing helix chain 'N' and resid 113 through 117 Processing helix chain 'O' and resid 38 through 50 Processing helix chain 'O' and resid 56 through 85 removed outlier: 3.864A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 103 Processing helix chain 'O' and resid 104 through 125 removed outlier: 3.816A pdb=" N SER O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 58 removed outlier: 3.569A pdb=" N ARG P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 77 removed outlier: 3.555A pdb=" N GLN P 77 " --> pdb=" O ARG P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 115 removed outlier: 3.862A pdb=" N VAL P 90 " --> pdb=" O GLN P 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU P 110 " --> pdb=" O GLU P 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 115 " --> pdb=" O CYS P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 133 removed outlier: 3.669A pdb=" N ILE P 125 " --> pdb=" O MET P 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 30 removed outlier: 4.140A pdb=" N ILE Q 27 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 42 Processing helix chain 'Q' and resid 50 through 77 removed outlier: 3.836A pdb=" N GLU Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE Q 62 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP Q 69 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 95 removed outlier: 3.639A pdb=" N VAL Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 23 Processing helix chain 'R' and resid 27 through 37 Processing helix chain 'R' and resid 47 through 73 Processing helix chain 'R' and resid 80 through 90 Processing helix chain 'R' and resid 93 through 98 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'S' and resid 56 through 85 removed outlier: 3.510A pdb=" N ILE S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL S 67 " --> pdb=" O MET S 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN S 68 " --> pdb=" O ASN S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 103 Processing helix chain 'S' and resid 104 through 125 removed outlier: 3.656A pdb=" N LYS S 109 " --> pdb=" O GLY S 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.589A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.527A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.099A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.954A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.219A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'L' and resid 84 through 85 removed outlier: 6.590A pdb=" N ARG L 84 " --> pdb=" O VAL M 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 119 through 120 removed outlier: 3.525A pdb=" N ILE L 120 " --> pdb=" O ARG M 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB5, first strand: chain 'N' and resid 43 through 44 removed outlier: 7.100A pdb=" N ARG N 43 " --> pdb=" O ILE O 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'N' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'P' and resid 84 through 85 removed outlier: 6.953A pdb=" N ARG P 84 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'P' and resid 119 through 120 Processing sheet with id=AC1, first strand: chain 'R' and resid 43 through 44 removed outlier: 7.219A pdb=" N ARG R 43 " --> pdb=" O ILE S 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'R' and resid 78 through 79 752 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 724 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 282 basepair parallelities 524 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18926 1.03 - 1.23: 223 1.23 - 1.42: 10728 1.42 - 1.61: 14211 1.61 - 1.81: 48 Bond restraints: 44136 Sorted by residual: bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.50e+01 bond pdb=" C3' DC X 69 " pdb=" C2' DC X 69 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.34e+01 bond pdb=" C3' DA X -5 " pdb=" C2' DA X -5 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.20e+01 bond pdb=" C3' DA I -5 " pdb=" C2' DA I -5 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.19e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 1.99e+01 ... (remaining 44131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 69397 1.32 - 2.64: 9370 2.64 - 3.97: 959 3.97 - 5.29: 264 5.29 - 6.61: 14 Bond angle restraints: 80004 Sorted by residual: angle pdb=" O4' DC X 66 " pdb=" C1' DC X 66 " pdb=" N1 DC X 66 " ideal model delta sigma weight residual 108.00 113.12 -5.12 7.00e-01 2.04e+00 5.35e+01 angle pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " pdb=" N1 DC I 66 " ideal model delta sigma weight residual 108.00 113.12 -5.12 7.00e-01 2.04e+00 5.34e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 112.95 -4.95 7.00e-01 2.04e+00 5.00e+01 angle pdb=" O4' DG Y 27 " pdb=" C1' DG Y 27 " pdb=" N9 DG Y 27 " ideal model delta sigma weight residual 108.00 112.90 -4.90 7.00e-01 2.04e+00 4.90e+01 angle pdb=" O4' DT I 34 " pdb=" C1' DT I 34 " pdb=" N1 DT I 34 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.98e+01 ... (remaining 79999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 12852 17.18 - 34.36: 2401 34.36 - 51.54: 1836 51.54 - 68.72: 1213 68.72 - 85.90: 26 Dihedral angle restraints: 18328 sinusoidal: 13456 harmonic: 4872 Sorted by residual: dihedral pdb=" CG ARG H 100 " pdb=" CD ARG H 100 " pdb=" NE ARG H 100 " pdb=" CZ ARG H 100 " ideal model delta sinusoidal sigma weight residual -90.00 -43.90 -46.10 2 1.50e+01 4.44e-03 1.11e+01 dihedral pdb=" CG ARG S 100 " pdb=" CD ARG S 100 " pdb=" NE ARG S 100 " pdb=" CZ ARG S 100 " ideal model delta sinusoidal sigma weight residual -90.00 -43.91 -46.09 2 1.50e+01 4.44e-03 1.11e+01 dihedral pdb=" CG ARG F 56 " pdb=" CD ARG F 56 " pdb=" NE ARG F 56 " pdb=" CZ ARG F 56 " ideal model delta sinusoidal sigma weight residual 180.00 135.59 44.41 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 18325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2315 0.043 - 0.086: 1107 0.086 - 0.129: 521 0.129 - 0.172: 174 0.172 - 0.215: 27 Chirality restraints: 4144 Sorted by residual: chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C4' DC I 69 " pdb=" C5' DC I 69 " pdb=" O4' DC I 69 " pdb=" C3' DC I 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C4' DC X 21 " pdb=" C5' DC X 21 " pdb=" O4' DC X 21 " pdb=" C3' DC X 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4141 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 33 " -0.023 9.50e-02 1.11e+02 3.95e-02 3.39e+01 pdb=" NE ARG N 33 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG N 33 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG N 33 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG N 33 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG N 33 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG N 33 " 0.074 2.00e-02 2.50e+03 pdb="HH21 ARG N 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG N 33 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " 0.023 9.50e-02 1.11e+02 3.94e-02 3.37e+01 pdb=" NE ARG C 33 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 33 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG C 33 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 33 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 33 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG C 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 87 " -0.409 9.50e-02 1.11e+02 1.39e-01 3.27e+01 pdb=" NE ARG S 87 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG S 87 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG S 87 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG S 87 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG S 87 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG S 87 " -0.018 2.00e-02 2.50e+03 pdb="HH21 ARG S 87 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG S 87 " -0.045 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1182 2.19 - 2.79: 69322 2.79 - 3.39: 99155 3.39 - 4.00: 140983 4.00 - 4.60: 223294 Nonbonded interactions: 533936 Sorted by model distance: nonbonded pdb=" OE1 GLU E 74 " pdb="HD21 ASN F 26 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU P 74 " pdb="HD21 ASN Q 26 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP P 107 " pdb="HH11 ARG P 132 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP O 69 " pdb=" HH TYR Q 99 " model vdw 1.611 2.450 ... (remaining 533931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) selection = chain 'M' selection = (chain 'Q' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.030 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4822 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 : 0.007 0.069 25202 Z= 0.619 Angle : 1.019 6.610 36484 Z= 0.862 Chirality : 0.062 0.215 4144 Planarity : 0.013 0.152 2636 Dihedral : 26.172 85.903 10870 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1472 helix: 0.46 (0.14), residues: 1062 sheet: None (None), residues: 0 loop : -0.33 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG E 64 TYR 0.020 0.005 TYR G 58 PHE 0.017 0.003 PHE O 66 HIS 0.012 0.003 HIS O 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.62 (25202) covalent geometry : angle 1.01930 / 0.86 (36484) hydrogen bonds : bond 0.13250 / 8.98 ( 1476) hydrogen bonds : angle 3.77986 / 2.75 ( 3662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.9336 (mt) cc_final: 0.9107 (mm) REVERT: B 97 THR cc_start: 0.6319 (m) cc_final: 0.5810 (p) REVERT: F 65 ASN cc_start: 0.9115 (m-40) cc_final: 0.8877 (m110) REVERT: G 96 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8753 (tttt) REVERT: H 52 ASP cc_start: 0.7923 (p0) cc_final: 0.7637 (p0) REVERT: M 65 ASN cc_start: 0.8735 (m-40) cc_final: 0.8459 (p0) REVERT: M 88 VAL cc_start: 0.8726 (t) cc_final: 0.8519 (p) REVERT: O 114 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8105 (mm-30) outliers start: 2 outliers final: 0 residues processed: 444 average time/residue: 0.4233 time to fit residues: 262.6618 Evaluate side-chains 257 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 overall best weight: 6.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN C 90 ASN D 96 GLN L 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.112397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.088281 restraints weight = 323588.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.091622 restraints weight = 165988.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.093774 restraints weight = 103426.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.095226 restraints weight = 73649.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.096222 restraints weight = 57344.926| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25202 Z= 0.238 Angle : 0.756 7.263 36484 Z= 0.484 Chirality : 0.048 0.171 4144 Planarity : 0.006 0.056 2636 Dihedral : 29.315 84.509 7918 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.77 % Allowed : 12.96 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1472 helix: 1.17 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.58 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 100 TYR 0.035 0.002 TYR N 51 PHE 0.014 0.002 PHE S 71 HIS 0.013 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.24 (25202) covalent geometry : angle 0.75645 / 0.48 (36484) hydrogen bonds : bond 0.08679 / 5.80 ( 1476) hydrogen bonds : angle 3.92086 / 2.88 ( 3662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 THR cc_start: 0.6467 (m) cc_final: 0.6264 (t) REVERT: C 94 LEU cc_start: 0.7462 (mt) cc_final: 0.7246 (mt) REVERT: D 106 GLU cc_start: 0.8695 (pm20) cc_final: 0.8310 (pm20) REVERT: G 96 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8867 (tmtt) REVERT: H 52 ASP cc_start: 0.8581 (p0) cc_final: 0.8338 (p0) REVERT: P 75 ILE cc_start: 0.8794 (mt) cc_final: 0.8415 (tt) REVERT: R 98 LEU cc_start: 0.7247 (mt) cc_final: 0.6907 (mt) outliers start: 22 outliers final: 18 residues processed: 282 average time/residue: 0.4176 time to fit residues: 167.2316 Evaluate side-chains 260 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain S residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 164 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS O 96 GLN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.106931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.082585 restraints weight = 330111.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.085673 restraints weight = 167213.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.087722 restraints weight = 104194.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.089108 restraints weight = 74006.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.090027 restraints weight = 57714.902| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25202 Z= 0.204 Angle : 0.693 8.574 36484 Z= 0.453 Chirality : 0.044 0.190 4144 Planarity : 0.006 0.099 2636 Dihedral : 30.119 89.904 7918 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.77 % Allowed : 11.76 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1472 helix: 1.01 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -0.83 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 100 TYR 0.019 0.002 TYR F 73 PHE 0.022 0.003 PHE M 62 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.20 (25202) covalent geometry : angle 0.69252 / 0.45 (36484) hydrogen bonds : bond 0.08463 / 5.60 ( 1476) hydrogen bonds : angle 3.80628 / 2.79 ( 3662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASN cc_start: 0.7275 (m-40) cc_final: 0.6952 (m-40) REVERT: G 62 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8594 (tm-30) REVERT: G 96 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8801 (tttt) REVERT: L 68 PHE cc_start: 0.7309 (t80) cc_final: 0.7091 (t80) REVERT: N 62 GLU cc_start: 0.9251 (tp30) cc_final: 0.8760 (tm-30) REVERT: R 98 LEU cc_start: 0.7319 (mt) cc_final: 0.7097 (mt) outliers start: 22 outliers final: 14 residues processed: 255 average time/residue: 0.4119 time to fit residues: 147.6542 Evaluate side-chains 230 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 74 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 195 optimal weight: 50.0000 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.101423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.077337 restraints weight = 344821.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.080242 restraints weight = 173410.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.082156 restraints weight = 107707.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.083426 restraints weight = 76903.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.084296 restraints weight = 60493.733| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25202 Z= 0.257 Angle : 0.742 6.793 36484 Z= 0.465 Chirality : 0.047 0.184 4144 Planarity : 0.006 0.115 2636 Dihedral : 30.373 88.425 7918 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 14.33 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1472 helix: 0.53 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 117 TYR 0.025 0.002 TYR A 55 PHE 0.017 0.003 PHE A 105 HIS 0.012 0.002 HIS R 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.26 (25202) covalent geometry : angle 0.74237 / 0.47 (36484) hydrogen bonds : bond 0.11629 / 7.64 ( 1476) hydrogen bonds : angle 4.07862 / 2.98 ( 3662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASN cc_start: 0.7520 (m-40) cc_final: 0.7218 (m-40) REVERT: C 94 LEU cc_start: 0.7801 (mt) cc_final: 0.7499 (mt) REVERT: C 113 GLN cc_start: 0.9024 (tp40) cc_final: 0.8606 (tm-30) REVERT: D 63 MET cc_start: 0.8273 (mmp) cc_final: 0.8062 (mmp) REVERT: D 106 GLU cc_start: 0.9324 (mp0) cc_final: 0.8825 (pm20) REVERT: G 62 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8609 (tm-30) REVERT: G 96 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8863 (tmtt) REVERT: N 62 GLU cc_start: 0.9279 (tp30) cc_final: 0.8876 (tm-30) REVERT: Q 68 ARG cc_start: 0.9455 (ttm110) cc_final: 0.9196 (ttm110) REVERT: R 98 LEU cc_start: 0.7337 (mt) cc_final: 0.7126 (mt) outliers start: 37 outliers final: 28 residues processed: 226 average time/residue: 0.4596 time to fit residues: 147.0386 Evaluate side-chains 225 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 69 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 99 optimal weight: 40.0000 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN P 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.102393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.078273 restraints weight = 346263.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.081235 restraints weight = 172491.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.083212 restraints weight = 106674.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.084536 restraints weight = 75755.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.085419 restraints weight = 59299.854| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25202 Z= 0.176 Angle : 0.647 9.494 36484 Z= 0.422 Chirality : 0.043 0.166 4144 Planarity : 0.005 0.042 2636 Dihedral : 30.574 89.500 7918 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.17 % Allowed : 15.62 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1472 helix: 1.10 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 117 TYR 0.027 0.002 TYR P 100 PHE 0.027 0.002 PHE R 26 HIS 0.005 0.001 HIS O 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.18 (25202) covalent geometry : angle 0.64691 / 0.42 (36484) hydrogen bonds : bond 0.07751 / 5.07 ( 1476) hydrogen bonds : angle 3.78525 / 2.79 ( 3662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASN cc_start: 0.7465 (m-40) cc_final: 0.7182 (m-40) REVERT: G 62 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8643 (tm-30) REVERT: G 96 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8848 (tmtt) REVERT: N 62 GLU cc_start: 0.9309 (tp30) cc_final: 0.8895 (tm-30) REVERT: P 100 TYR cc_start: 0.7833 (t80) cc_final: 0.7428 (t80) outliers start: 27 outliers final: 24 residues processed: 223 average time/residue: 0.4318 time to fit residues: 135.8792 Evaluate side-chains 219 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 63 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 196 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.099928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.075676 restraints weight = 355198.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.078562 restraints weight = 177419.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.080446 restraints weight = 110593.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.081695 restraints weight = 79270.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.082518 restraints weight = 62735.290| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25202 Z= 0.210 Angle : 0.674 8.497 36484 Z= 0.432 Chirality : 0.043 0.265 4144 Planarity : 0.005 0.086 2636 Dihedral : 30.637 88.198 7918 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 15.94 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1472 helix: 0.87 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 36 TYR 0.028 0.002 TYR P 100 PHE 0.026 0.002 PHE Q 62 HIS 0.013 0.002 HIS R 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.21 (25202) covalent geometry : angle 0.67417 / 0.43 (36484) hydrogen bonds : bond 0.09229 / 6.05 ( 1476) hydrogen bonds : angle 3.92391 / 2.89 ( 3662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASN cc_start: 0.7570 (m-40) cc_final: 0.7299 (m-40) REVERT: D 63 MET cc_start: 0.8247 (mmp) cc_final: 0.8012 (mmp) REVERT: D 106 GLU cc_start: 0.9268 (mp0) cc_final: 0.8588 (pm20) REVERT: G 96 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8856 (tmtt) REVERT: H 93 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7494 (mpp-170) REVERT: L 68 PHE cc_start: 0.7471 (t80) cc_final: 0.7193 (t80) REVERT: N 62 GLU cc_start: 0.9370 (tp30) cc_final: 0.8975 (tm-30) REVERT: P 100 TYR cc_start: 0.7900 (t80) cc_final: 0.7643 (t80) outliers start: 32 outliers final: 27 residues processed: 218 average time/residue: 0.4659 time to fit residues: 143.0188 Evaluate side-chains 216 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 197 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 180 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 190 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 HIS ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.071667 restraints weight = 357840.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.074527 restraints weight = 181026.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.076445 restraints weight = 111449.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.077663 restraints weight = 78666.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.078481 restraints weight = 61744.499| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 25202 Z= 0.202 Angle : 0.679 12.618 36484 Z= 0.434 Chirality : 0.043 0.296 4144 Planarity : 0.006 0.142 2636 Dihedral : 30.920 89.895 7918 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.98 % Allowed : 16.51 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1472 helix: 0.90 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 117 TYR 0.032 0.002 TYR M 89 PHE 0.023 0.002 PHE R 26 HIS 0.006 0.002 HIS R 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.20 (25202) covalent geometry : angle 0.67872 / 0.43 (36484) hydrogen bonds : bond 0.08477 / 5.59 ( 1476) hydrogen bonds : angle 3.97496 / 2.92 ( 3662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASN cc_start: 0.7667 (m-40) cc_final: 0.7383 (m-40) REVERT: G 96 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8860 (tmtt) REVERT: L 68 PHE cc_start: 0.7647 (t80) cc_final: 0.7330 (t80) REVERT: N 62 GLU cc_start: 0.9423 (tp30) cc_final: 0.9065 (tm-30) REVERT: P 100 TYR cc_start: 0.8092 (t80) cc_final: 0.7581 (t80) REVERT: R 95 ASN cc_start: 0.7981 (t0) cc_final: 0.7708 (m-40) outliers start: 37 outliers final: 32 residues processed: 218 average time/residue: 0.4248 time to fit residues: 131.2160 Evaluate side-chains 216 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 192 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN D 110 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN P 126 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.093715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.068983 restraints weight = 367534.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.071725 restraints weight = 185934.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.073541 restraints weight = 114777.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.074689 restraints weight = 81252.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.075465 restraints weight = 63965.053| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25202 Z= 0.251 Angle : 0.725 7.280 36484 Z= 0.454 Chirality : 0.044 0.180 4144 Planarity : 0.006 0.069 2636 Dihedral : 30.999 89.259 7918 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 2.90 % Allowed : 16.99 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1472 helix: 0.39 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 68 TYR 0.027 0.002 TYR M 89 PHE 0.017 0.002 PHE Q 62 HIS 0.017 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.25 (25202) covalent geometry : angle 0.72532 / 0.45 (36484) hydrogen bonds : bond 0.11607 / 7.63 ( 1476) hydrogen bonds : angle 4.28349 / 3.14 ( 3662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 96 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8889 (tmtt) REVERT: L 68 PHE cc_start: 0.7757 (t80) cc_final: 0.7406 (t80) REVERT: M 75 GLU cc_start: 0.9326 (tp30) cc_final: 0.9029 (tm-30) REVERT: N 62 GLU cc_start: 0.9432 (tp30) cc_final: 0.9089 (tm-30) REVERT: P 100 TYR cc_start: 0.8126 (t80) cc_final: 0.7807 (t80) REVERT: R 95 ASN cc_start: 0.8018 (t0) cc_final: 0.7744 (m-40) outliers start: 36 outliers final: 32 residues processed: 206 average time/residue: 0.4198 time to fit residues: 121.3432 Evaluate side-chains 206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 80 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.095123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.070897 restraints weight = 378932.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.073603 restraints weight = 191516.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.075373 restraints weight = 120302.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.076504 restraints weight = 86310.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.077252 restraints weight = 68619.295| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.7277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25202 Z= 0.178 Angle : 0.655 9.200 36484 Z= 0.420 Chirality : 0.042 0.156 4144 Planarity : 0.005 0.043 2636 Dihedral : 31.088 89.348 7918 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.25 % Allowed : 18.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1472 helix: 0.88 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 68 TYR 0.026 0.002 TYR M 89 PHE 0.013 0.002 PHE D 66 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.18 (25202) covalent geometry : angle 0.65484 / 0.42 (36484) hydrogen bonds : bond 0.08148 / 5.35 ( 1476) hydrogen bonds : angle 3.96037 / 2.91 ( 3662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 96 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8837 (tmtt) REVERT: L 68 PHE cc_start: 0.7778 (t80) cc_final: 0.7418 (t80) REVERT: N 62 GLU cc_start: 0.9414 (tp30) cc_final: 0.9084 (tm-30) REVERT: P 100 TYR cc_start: 0.8102 (t80) cc_final: 0.7622 (t80) REVERT: R 95 ASN cc_start: 0.7979 (t0) cc_final: 0.7717 (m-40) outliers start: 28 outliers final: 28 residues processed: 199 average time/residue: 0.4079 time to fit residues: 115.2617 Evaluate side-chains 202 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 175 optimal weight: 30.0000 chunk 170 optimal weight: 50.0000 chunk 176 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.093325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.069223 restraints weight = 382691.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.071873 restraints weight = 193810.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.073607 restraints weight = 121462.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.074704 restraints weight = 87136.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.075441 restraints weight = 69308.649| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25202 Z= 0.212 Angle : 0.685 8.839 36484 Z= 0.432 Chirality : 0.042 0.267 4144 Planarity : 0.005 0.058 2636 Dihedral : 31.065 89.821 7918 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 2.25 % Allowed : 18.52 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1472 helix: 0.80 (0.15), residues: 1084 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 68 TYR 0.021 0.002 TYR E 100 PHE 0.018 0.002 PHE L 105 HIS 0.015 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.21 (25202) covalent geometry : angle 0.68501 / 0.43 (36484) hydrogen bonds : bond 0.09793 / 6.42 ( 1476) hydrogen bonds : angle 4.01414 / 2.94 ( 3662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 MET cc_start: 0.8259 (mmp) cc_final: 0.8052 (mmp) REVERT: G 96 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8855 (tmtt) REVERT: L 68 PHE cc_start: 0.7791 (t80) cc_final: 0.7433 (t80) REVERT: M 54 GLU cc_start: 0.7141 (tt0) cc_final: 0.6923 (tt0) REVERT: N 62 GLU cc_start: 0.9445 (tp30) cc_final: 0.9131 (tm-30) REVERT: P 100 TYR cc_start: 0.8143 (t80) cc_final: 0.7611 (t80) REVERT: R 95 ASN cc_start: 0.7986 (t0) cc_final: 0.7717 (m-40) outliers start: 28 outliers final: 27 residues processed: 201 average time/residue: 0.4151 time to fit residues: 118.8287 Evaluate side-chains 206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 187 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 143 optimal weight: 0.0270 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.093631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.070345 restraints weight = 413462.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.072927 restraints weight = 217308.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.074483 restraints weight = 136618.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.075579 restraints weight = 99953.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.076268 restraints weight = 79381.777| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25202 Z= 0.177 Angle : 0.646 6.807 36484 Z= 0.415 Chirality : 0.041 0.221 4144 Planarity : 0.005 0.072 2636 Dihedral : 31.124 88.342 7918 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.25 % Allowed : 18.76 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1472 helix: 0.99 (0.15), residues: 1084 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 79 TYR 0.021 0.002 TYR M 89 PHE 0.014 0.002 PHE L 105 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.18 (25202) covalent geometry : angle 0.64580 / 0.41 (36484) hydrogen bonds : bond 0.08020 / 5.27 ( 1476) hydrogen bonds : angle 3.88683 / 2.85 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9915.49 seconds wall clock time: 168 minutes 30.81 seconds (10110.81 seconds total)