Starting phenix.real_space_refine on Tue Jul 7 03:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmn_48395/07_2026/9mmn_48395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmn_48395/07_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_48395/07_2026/9mmn_48395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmn_48395/07_2026/9mmn_48395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmn_48395/07_2026/9mmn_48395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmn_48395/07_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-dev-6108/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: 6.56, per 1000 atoms: 0.15 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: 3.59 Conformation dependent library (CDL) restraints added in 817.1 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: 7.04 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: 10.65 Time building geometry restraints manager: 4.85 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: 69531 1.32 - 2.64: 9301 2.64 - 3.97: 896 3.97 - 5.29: 262 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: 4.560 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: 0.240 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 42.880 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.520 ------------------------------------------------------------------------------- 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= 0.618 Angle : 1.006 6.610 36484 Z= 0.847 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 1.00593 / 0.85 (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 : 0.914 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: 0.8878 (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: 0.7635 (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: 0.8518 (p) REVERT: O 114 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8106 (mm-30) outliers start: 2 outliers final: 0 residues processed: 444 average time/residue: 0.4482 time to fit residues: 277.2023 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 : 0.867 ------------------------------------------------------------------------------- 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: 20.0000 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 ** P 126 GLN ** 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 = 0.4968 r_free = 0.4968 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.087771 restraints weight = 322758.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.091076 restraints weight = 165446.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.093215 restraints weight = 102934.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.094656 restraints weight = 73107.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.095643 restraints weight = 56951.877| |-----------------------------------------------------------------------------| r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.3157 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= 0.239 Angle : 0.781 8.344 36484 Z= 0.489 Chirality : 0.051 0.185 4144 Planarity : 0.006 0.056 2636 Dihedral : 29.339 85.308 7918 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.85 % Allowed : 12.88 % 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: 0.90 (0.20), residues: 1472 helix: 1.08 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -0.56 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 80 TYR 0.018 0.002 TYR F 73 PHE 0.013 0.002 PHE S 71 HIS 0.014 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.24 (25202) covalent geometry : angle 0.78086 / 0.49 (36484) hydrogen bonds : bond 0.09049 / 6.03 ( 1476) hydrogen bonds : angle 3.87128 / 2.85 ( 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 293 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.871 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: B 97 THR cc_start: 0.6467 (m) cc_final: 0.6231 (t) REVERT: C 94 LEU cc_start: 0.7465 (mt) cc_final: 0.7251 (mt) REVERT: D 106 GLU cc_start: 0.8768 (pm20) cc_final: 0.8377 (pm20) REVERT: G 96 LYS cc_start: 0.9110 (ttmm) cc_final: 0.8836 (tmtt) REVERT: M 65 ASN cc_start: 0.9100 (m-40) cc_final: 0.8764 (p0) REVERT: O 63 MET cc_start: 0.8351 (mpp) cc_final: 0.8150 (mpp) REVERT: P 75 ILE cc_start: 0.8802 (mt) cc_final: 0.8426 (tt) REVERT: R 98 LEU cc_start: 0.7163 (mt) cc_final: 0.6833 (mt) outliers start: 23 outliers final: 18 residues processed: 285 average time/residue: 0.4489 time to fit residues: 180.9520 Evaluate side-chains 255 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 P residue 68 PHE Chi-restraints excluded: chain R residue 85 GLN 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: 10.0000 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.110813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.086963 restraints weight = 332581.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.090171 restraints weight = 168338.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.092302 restraints weight = 104843.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.093707 restraints weight = 74462.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.094675 restraints weight = 58344.945| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25202 Z= 0.172 Angle : 0.640 7.181 36484 Z= 0.430 Chirality : 0.042 0.177 4144 Planarity : 0.005 0.059 2636 Dihedral : 29.779 87.247 7918 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.21 % Allowed : 13.37 % Favored : 85.43 % 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: 1.41 (0.21), residues: 1472 helix: 1.52 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -0.58 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 40 TYR 0.016 0.002 TYR F 73 PHE 0.017 0.002 PHE D 66 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.17 (25202) covalent geometry : angle 0.64004 / 0.43 (36484) hydrogen bonds : bond 0.06641 / 4.41 ( 1476) hydrogen bonds : angle 3.49563 / 2.57 ( 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 257 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 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: A 55 TYR cc_start: 0.8568 (m-80) cc_final: 0.8333 (m-80) REVERT: A 83 LEU cc_start: 0.5713 (mt) cc_final: 0.5045 (mt) REVERT: B 97 THR cc_start: 0.6700 (m) cc_final: 0.6444 (t) REVERT: C 69 ASN cc_start: 0.7121 (m-40) cc_final: 0.6766 (m-40) REVERT: C 94 LEU cc_start: 0.7529 (mt) cc_final: 0.7274 (mt) REVERT: G 96 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8866 (ttpt) REVERT: H 91 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.6002 (t) REVERT: M 65 ASN cc_start: 0.9132 (m-40) cc_final: 0.8801 (p0) REVERT: N 62 GLU cc_start: 0.9177 (tp30) cc_final: 0.8712 (tm-30) REVERT: R 98 LEU cc_start: 0.7155 (mt) cc_final: 0.6813 (mt) outliers start: 15 outliers final: 10 residues processed: 253 average time/residue: 0.4550 time to fit residues: 163.5950 Evaluate side-chains 229 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP 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 69 ASP Chi-restraints excluded: chain H residue 91 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 68 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 195 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN ** S 68 ASN ** 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 = 0.4879 r_free = 0.4879 target = 0.102549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.078334 restraints weight = 342531.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.081265 restraints weight = 174654.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.083205 restraints weight = 109462.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.084496 restraints weight = 78265.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.085357 restraints weight = 61656.892| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 25202 Z= 0.278 Angle : 0.762 9.687 36484 Z= 0.477 Chirality : 0.047 0.235 4144 Planarity : 0.006 0.054 2636 Dihedral : 30.205 89.046 7918 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.66 % Allowed : 13.45 % Favored : 83.90 % 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: 0.11 (0.20), residues: 1472 helix: 0.64 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 79 TYR 0.021 0.003 TYR F 73 PHE 0.023 0.003 PHE A 105 HIS 0.016 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.28 (25202) covalent geometry : angle 0.76238 / 0.48 (36484) hydrogen bonds : bond 0.12411 / 8.18 ( 1476) hydrogen bonds : angle 4.08164 / 2.99 ( 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 248 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.927 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: A 55 TYR cc_start: 0.8593 (m-80) cc_final: 0.8387 (m-80) REVERT: C 69 ASN cc_start: 0.7463 (m-40) cc_final: 0.7112 (m-40) REVERT: C 113 GLN cc_start: 0.9060 (tp40) cc_final: 0.8832 (tm-30) REVERT: G 62 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8642 (tm-30) REVERT: G 96 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8847 (tttt) REVERT: N 62 GLU cc_start: 0.9275 (tp30) cc_final: 0.8811 (tm-30) outliers start: 33 outliers final: 28 residues processed: 233 average time/residue: 0.4627 time to fit residues: 152.3039 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 : 0.946 ------------------------------------------------------------------------------- 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 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 D residue 66 PHE Chi-restraints excluded: chain D residue 94 GLU 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 36 GLU 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 59 LEU Chi-restraints excluded: chain N residue 91 ASP 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 P residue 78 ASP Chi-restraints excluded: chain R residue 59 LEU 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: 1.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 chunk 162 optimal weight: 0.3980 chunk 145 optimal weight: 40.0000 chunk 99 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN ** S 68 ASN ** 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 = 0.4907 r_free = 0.4907 target = 0.104905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.080717 restraints weight = 341834.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.083782 restraints weight = 171602.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.085811 restraints weight = 106204.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.087146 restraints weight = 75356.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.088053 restraints weight = 59115.547| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25202 Z= 0.161 Angle : 0.625 9.549 36484 Z= 0.411 Chirality : 0.042 0.159 4144 Planarity : 0.005 0.050 2636 Dihedral : 30.388 88.458 7918 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.61 % Allowed : 16.43 % Favored : 81.96 % 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: 1.10 (0.21), residues: 1472 helix: 1.41 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 73 TYR 0.017 0.001 TYR F 73 PHE 0.014 0.002 PHE D 66 HIS 0.005 0.001 HIS R 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.16 (25202) covalent geometry : angle 0.62482 / 0.41 (36484) hydrogen bonds : bond 0.06898 / 4.51 ( 1476) hydrogen bonds : angle 3.56651 / 2.62 ( 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 226 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.851 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: A 55 TYR cc_start: 0.8565 (m-80) cc_final: 0.8312 (m-80) REVERT: C 69 ASN cc_start: 0.7505 (m-40) cc_final: 0.7151 (m-40) REVERT: G 62 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8630 (tm-30) REVERT: G 96 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8827 (tmtt) REVERT: N 62 GLU cc_start: 0.9262 (tp30) cc_final: 0.8832 (tm-30) outliers start: 20 outliers final: 19 residues processed: 218 average time/residue: 0.4510 time to fit residues: 138.2721 Evaluate side-chains 216 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 93 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 59 LEU 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 M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain R residue 59 LEU 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: 10.0000 chunk 7 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 110 HIS G 111 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.100326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.075767 restraints weight = 347335.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.078622 restraints weight = 176881.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.080481 restraints weight = 111080.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.081735 restraints weight = 80056.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.082578 restraints weight = 63531.749| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 25202 Z= 0.235 Angle : 0.689 8.020 36484 Z= 0.440 Chirality : 0.044 0.280 4144 Planarity : 0.005 0.058 2636 Dihedral : 30.533 88.104 7918 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 2.74 % Allowed : 15.78 % 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: 0.31 (0.20), residues: 1472 helix: 0.84 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.034 0.002 TYR P 100 PHE 0.031 0.003 PHE Q 62 HIS 0.010 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.23 (25202) covalent geometry : angle 0.68925 / 0.44 (36484) hydrogen bonds : bond 0.10334 / 6.79 ( 1476) hydrogen bonds : angle 3.96017 / 2.91 ( 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 229 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.896 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: A 55 TYR cc_start: 0.8636 (m-80) cc_final: 0.8416 (m-80) REVERT: A 130 ARG cc_start: 0.8344 (mmp-170) cc_final: 0.7932 (mmm160) REVERT: C 69 ASN cc_start: 0.7534 (m-40) cc_final: 0.7184 (m-40) REVERT: D 63 MET cc_start: 0.8128 (mmp) cc_final: 0.7788 (mmp) REVERT: G 62 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8723 (tm-30) REVERT: G 96 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8873 (tmtt) REVERT: N 62 GLU cc_start: 0.9311 (tp30) cc_final: 0.8919 (tm-30) outliers start: 34 outliers final: 28 residues processed: 214 average time/residue: 0.4790 time to fit residues: 143.2844 Evaluate side-chains 215 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 B residue 75 GLU Chi-restraints excluded: chain B residue 85 MET 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 D residue 66 PHE Chi-restraints excluded: chain E residue 91 MET 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 36 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 123 THR 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 N residue 91 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 69 ASP 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: 5.9990 chunk 37 optimal weight: 4.9990 chunk 197 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 chunk 180 optimal weight: 40.0000 chunk 31 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 190 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 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 = 0.4762 r_free = 0.4762 target = 0.097710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.072883 restraints weight = 366735.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.075817 restraints weight = 183146.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.077726 restraints weight = 112056.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.078964 restraints weight = 79031.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.079782 restraints weight = 61957.894| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25202 Z= 0.198 Angle : 0.662 6.992 36484 Z= 0.427 Chirality : 0.043 0.161 4144 Planarity : 0.006 0.141 2636 Dihedral : 30.867 88.844 7918 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.25 % Allowed : 17.23 % 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: 0.45 (0.21), residues: 1472 helix: 0.93 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.35 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 117 TYR 0.024 0.002 TYR P 100 PHE 0.016 0.002 PHE D 71 HIS 0.004 0.001 HIS C 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (25202) covalent geometry : angle 0.66237 / 0.43 (36484) hydrogen bonds : bond 0.08343 / 5.50 ( 1476) hydrogen bonds : angle 3.96553 / 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 221 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.738 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: 0.7642 (m-40) cc_final: 0.7307 (m-40) REVERT: C 113 GLN cc_start: 0.8902 (tp40) cc_final: 0.8655 (tp40) REVERT: G 96 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8880 (tmtt) REVERT: L 68 PHE cc_start: 0.7626 (t80) cc_final: 0.7322 (t80) REVERT: M 65 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8934 (p0) REVERT: N 62 GLU cc_start: 0.9386 (tp30) cc_final: 0.9016 (tm-30) REVERT: R 95 ASN cc_start: 0.7959 (t0) cc_final: 0.7686 (m-40) outliers start: 28 outliers final: 19 residues processed: 212 average time/residue: 0.4731 time to fit residues: 140.4543 Evaluate side-chains 206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 93 ARG 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 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 L residue 106 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 174 optimal weight: 40.0000 chunk 21 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** S 85 ASN ** 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 = 0.4719 r_free = 0.4719 target = 0.093817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.069386 restraints weight = 379780.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.072064 restraints weight = 191691.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.073829 restraints weight = 120305.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.074959 restraints weight = 86144.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.075727 restraints weight = 68367.359| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25202 Z= 0.270 Angle : 0.741 8.283 36484 Z= 0.465 Chirality : 0.045 0.211 4144 Planarity : 0.006 0.102 2636 Dihedral : 30.989 89.651 7918 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 17.71 % 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: -0.37 (0.20), residues: 1472 helix: 0.32 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.66 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 36 TYR 0.027 0.002 TYR M 89 PHE 0.017 0.003 PHE A 105 HIS 0.016 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.27 (25202) covalent geometry : angle 0.74088 / 0.46 (36484) hydrogen bonds : bond 0.12450 / 8.19 ( 1476) hydrogen bonds : angle 4.38027 / 3.21 ( 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: 32 poor density : 190 time to evaluate : 0.951 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: D 106 GLU cc_start: 0.9286 (mp0) cc_final: 0.8701 (pm20) REVERT: G 96 LYS cc_start: 0.9167 (ttmm) cc_final: 0.8900 (tmtt) REVERT: H 93 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7434 (mpp-170) REVERT: L 68 PHE cc_start: 0.7710 (t80) cc_final: 0.7389 (t80) REVERT: N 62 GLU cc_start: 0.9424 (tp30) cc_final: 0.9076 (tm-30) REVERT: O 60 MET cc_start: 0.5982 (tpt) cc_final: 0.5595 (tpt) REVERT: R 95 ASN cc_start: 0.8023 (t0) cc_final: 0.7725 (m-40) outliers start: 32 outliers final: 28 residues processed: 210 average time/residue: 0.4775 time to fit residues: 140.5430 Evaluate side-chains 206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 86 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 91 MET 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 H residue 107 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 46 LEU 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 67 VAL Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** M 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 = 0.4761 r_free = 0.4761 target = 0.097061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.072686 restraints weight = 377725.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.075403 restraints weight = 191278.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.077235 restraints weight = 120087.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.078397 restraints weight = 86211.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.079169 restraints weight = 68540.997| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25202 Z= 0.160 Angle : 0.637 6.846 36484 Z= 0.412 Chirality : 0.041 0.155 4144 Planarity : 0.005 0.058 2636 Dihedral : 31.053 88.879 7918 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.85 % Allowed : 18.84 % Favored : 79.31 % 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: 0.61 (0.21), residues: 1472 helix: 1.07 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.35 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 68 TYR 0.021 0.002 TYR F 73 PHE 0.024 0.002 PHE Q 62 HIS 0.008 0.001 HIS R 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.16 (25202) covalent geometry : angle 0.63703 / 0.41 (36484) hydrogen bonds : bond 0.07297 / 4.79 ( 1476) hydrogen bonds : angle 3.81976 / 2.80 ( 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 212 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.938 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: B 93 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7402 (ttp80) REVERT: C 69 ASN cc_start: 0.7730 (m-40) cc_final: 0.7410 (m-40) REVERT: D 106 GLU cc_start: 0.9278 (mp0) cc_final: 0.8686 (pm20) REVERT: G 96 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8835 (tmtt) REVERT: L 68 PHE cc_start: 0.7705 (t80) cc_final: 0.7366 (t80) REVERT: N 62 GLU cc_start: 0.9423 (tp30) cc_final: 0.9090 (tm-30) REVERT: R 95 ASN cc_start: 0.7925 (t0) cc_final: 0.7642 (m-40) outliers start: 23 outliers final: 20 residues processed: 204 average time/residue: 0.4716 time to fit residues: 135.8339 Evaluate side-chains 196 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 93 ARG 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 E residue 66 LEU Chi-restraints excluded: chain F residue 59 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 H residue 107 LEU Chi-restraints excluded: chain M residue 59 LEU 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 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 170 optimal weight: 40.0000 chunk 176 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 S 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.095933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.071572 restraints weight = 376378.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.074250 restraints weight = 194689.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.076067 restraints weight = 122083.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.077227 restraints weight = 87652.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.077980 restraints weight = 69471.444| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25202 Z= 0.183 Angle : 0.646 7.518 36484 Z= 0.415 Chirality : 0.041 0.257 4144 Planarity : 0.006 0.139 2636 Dihedral : 30.978 89.771 7918 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.85 % Allowed : 19.08 % Favored : 79.07 % 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: 0.65 (0.21), residues: 1472 helix: 1.08 (0.15), residues: 1084 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 21 TYR 0.018 0.002 TYR E 100 PHE 0.012 0.002 PHE Q 62 HIS 0.012 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (25202) covalent geometry : angle 0.64606 / 0.42 (36484) hydrogen bonds : bond 0.08202 / 5.38 ( 1476) hydrogen bonds : angle 3.85170 / 2.83 ( 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 202 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.914 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: B 93 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7388 (ttp80) REVERT: C 69 ASN cc_start: 0.7757 (m-40) cc_final: 0.7431 (m-40) REVERT: D 63 MET cc_start: 0.8217 (mmp) cc_final: 0.7906 (mmp) REVERT: D 106 GLU cc_start: 0.9276 (mp0) cc_final: 0.8682 (pm20) REVERT: G 96 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8843 (tmtt) REVERT: L 68 PHE cc_start: 0.7755 (t80) cc_final: 0.7411 (t80) REVERT: N 62 GLU cc_start: 0.9431 (tp30) cc_final: 0.9105 (tm-30) REVERT: R 95 ASN cc_start: 0.7945 (t0) cc_final: 0.7658 (m-40) outliers start: 23 outliers final: 21 residues processed: 195 average time/residue: 0.4654 time to fit residues: 128.2937 Evaluate side-chains 201 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 93 ARG 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 E residue 66 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 24 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 107 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 46 LEU 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 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: 20.0000 chunk 192 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 187 optimal weight: 50.0000 chunk 60 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.094044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.070568 restraints weight = 402993.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.073113 restraints weight = 210198.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.074765 restraints weight = 132428.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.075811 restraints weight = 96131.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.076526 restraints weight = 76982.544| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25202 Z= 0.193 Angle : 0.652 8.294 36484 Z= 0.419 Chirality : 0.041 0.222 4144 Planarity : 0.006 0.140 2636 Dihedral : 31.068 89.994 7918 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.77 % Allowed : 19.08 % Favored : 79.15 % 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: 0.48 (0.21), residues: 1472 helix: 0.99 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 21 TYR 0.020 0.002 TYR E 100 PHE 0.016 0.002 PHE Q 62 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.19 (25202) covalent geometry : angle 0.65161 / 0.42 (36484) hydrogen bonds : bond 0.08625 / 5.68 ( 1476) hydrogen bonds : angle 3.94682 / 2.90 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11130.60 seconds wall clock time: 189 minutes 12.65 seconds (11352.65 seconds total)