Starting phenix.real_space_refine on Sun Feb 8 08:01:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmn_48395/02_2026/9mmn_48395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmn_48395/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmn_48395/02_2026/9mmn_48395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmn_48395/02_2026/9mmn_48395.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmn_48395/02_2026/9mmn_48395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmn_48395/02_2026/9mmn_48395.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 570 5.49 5 S 28 5.16 5 C 13060 2.51 5 N 4428 2.21 5 O 5526 1.98 5 H 18934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 6.89, per 1000 atoms: 0.16 Number of scatterers: 42546 At special positions: 0 Unit cell: (126.28, 139.37, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 570 15.00 O 5526 8.00 N 4428 7.00 C 13060 6.00 H 18934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 836.4 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: 7.54 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: 9.22 Time building geometry restraints manager: 4.18 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=" N ARG F 24 " pdb=" CA ARG F 24 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" N SER O 33 " pdb=" CA SER O 33 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N ARG Q 24 " pdb=" CA ARG Q 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP M 25 " pdb=" CA ASP M 25 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 44131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 69994 1.32 - 2.64: 9216 2.64 - 3.97: 729 3.97 - 5.29: 59 5.29 - 6.61: 6 Bond angle restraints: 80004 Sorted by residual: angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 109.70 104.25 5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C4' DC X 21 " pdb=" O4' DC X 21 " pdb=" C1' DC X 21 " ideal model delta sigma weight residual 109.70 104.29 5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C4' DC X 66 " pdb=" O4' DC X 66 " pdb=" C1' DC X 66 " ideal model delta sigma weight residual 109.70 104.33 5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C4' DC I 66 " pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " ideal model delta sigma weight residual 109.70 104.39 5.31 1.50e+00 4.44e-01 1.25e+01 angle pdb=" C2' DC X 69 " pdb=" C1' DC X 69 " pdb=" N1 DC X 69 " ideal model delta sigma weight residual 113.50 118.52 -5.02 1.50e+00 4.44e-01 1.12e+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 - 0.048: 2887 0.048 - 0.095: 1030 0.095 - 0.143: 193 0.143 - 0.190: 24 0.190 - 0.238: 10 Chirality restraints: 4144 Sorted by residual: chirality pdb=" C1' DC X 66 " pdb=" O4' DC X 66 " pdb=" C2' DC X 66 " pdb=" N1 DC X 66 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.39e+00 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 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 4141 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 33 " -0.023 9.50e-02 1.11e+02 3.95e-02 3.39e+01 pdb=" NE ARG N 33 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG N 33 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG N 33 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG N 33 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG N 33 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG N 33 " 0.074 2.00e-02 2.50e+03 pdb="HH21 ARG N 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG N 33 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " 0.023 9.50e-02 1.11e+02 3.94e-02 3.37e+01 pdb=" NE ARG C 33 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 33 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG C 33 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 33 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 33 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG C 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 87 " -0.409 9.50e-02 1.11e+02 1.39e-01 3.27e+01 pdb=" NE ARG S 87 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG S 87 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG S 87 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG S 87 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG S 87 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG S 87 " -0.018 2.00e-02 2.50e+03 pdb="HH21 ARG S 87 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG S 87 " -0.045 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1182 2.19 - 2.79: 69322 2.79 - 3.39: 99155 3.39 - 4.00: 140983 4.00 - 4.60: 223294 Nonbonded interactions: 533936 Sorted by model distance: nonbonded pdb=" OE1 GLU E 74 " pdb="HD21 ASN F 26 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU P 74 " pdb="HD21 ASN Q 26 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP P 107 " pdb="HH11 ARG P 132 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP O 69 " pdb=" HH TYR Q 99 " model vdw 1.611 2.450 ... (remaining 533931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) selection = chain 'M' selection = (chain 'Q' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 40.080 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4944 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 : 0.005 0.069 25202 Z= 0.251 Angle : 0.913 6.610 36484 Z= 0.590 Chirality : 0.049 0.238 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 covalent geometry : bond 0.00532 (25202) covalent geometry : angle 0.91257 (36484) hydrogen bonds : bond 0.13250 ( 1476) hydrogen bonds : angle 3.77986 ( 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 : 0.898 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: 0.4805 time to fit residues: 292.2171 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 : 0.764 ------------------------------------------------------------------------------- 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: 9.9990 chunk 194 optimal weight: 10.0000 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: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN D 96 GLN F 76 HIS L 40 HIS M 76 HIS ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.102281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.077919 restraints weight = 345053.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.080895 restraints weight = 174685.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.082861 restraints weight = 108946.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.084160 restraints weight = 77759.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.085048 restraints weight = 61139.102| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 25202 Z= 0.318 Angle : 0.786 6.509 36484 Z= 0.483 Chirality : 0.049 0.187 4144 Planarity : 0.007 0.068 2636 Dihedral : 29.796 86.849 7918 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.33 % Allowed : 12.32 % Favored : 85.35 % 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: 0.73 (0.20), residues: 1472 helix: 0.91 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -0.47 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 132 TYR 0.024 0.003 TYR C 58 PHE 0.022 0.003 PHE F 101 HIS 0.011 0.002 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00672 (25202) covalent geometry : angle 0.78602 (36484) hydrogen bonds : bond 0.11630 ( 1476) hydrogen bonds : angle 4.02259 ( 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 285 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.873 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: A 56 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8795 (tp-100) REVERT: B 68 ARG cc_start: 0.9157 (ptp-110) cc_final: 0.8929 (ptp90) REVERT: C 69 ASN cc_start: 0.7546 (m-40) cc_final: 0.7222 (m-40) REVERT: C 94 LEU cc_start: 0.7656 (mt) cc_final: 0.7373 (mt) REVERT: G 62 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8702 (tm-30) REVERT: G 96 LYS cc_start: 0.9135 (ttmm) cc_final: 0.8837 (tmtt) REVERT: M 65 ASN cc_start: 0.9193 (m-40) cc_final: 0.8960 (p0) REVERT: N 62 GLU cc_start: 0.9276 (tp30) cc_final: 0.8796 (tm-30) outliers start: 29 outliers final: 23 residues processed: 275 average time/residue: 0.4838 time to fit residues: 183.4621 Evaluate side-chains 238 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain R residue 69 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 164 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN G 111 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.097353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.073144 restraints weight = 383855.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.075863 restraints weight = 197501.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.077683 restraints weight = 123461.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.078908 restraints weight = 87876.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.079703 restraints weight = 68340.043| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25202 Z= 0.250 Angle : 0.726 7.000 36484 Z= 0.449 Chirality : 0.043 0.165 4144 Planarity : 0.006 0.058 2636 Dihedral : 30.235 89.975 7918 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.38 % Allowed : 14.17 % Favored : 82.45 % 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: 0.71 (0.20), residues: 1472 helix: 1.05 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 96 TYR 0.023 0.002 TYR F 73 PHE 0.017 0.003 PHE F 101 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00527 (25202) covalent geometry : angle 0.72571 (36484) hydrogen bonds : bond 0.07551 ( 1476) hydrogen bonds : angle 3.97960 ( 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 258 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.848 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: D 106 GLU cc_start: 0.9377 (mp0) cc_final: 0.8771 (pm20) REVERT: G 96 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8794 (tmtt) REVERT: L 68 PHE cc_start: 0.7689 (t80) cc_final: 0.7399 (t80) REVERT: N 62 GLU cc_start: 0.9389 (tp30) cc_final: 0.9042 (tm-30) REVERT: P 100 TYR cc_start: 0.8044 (t80) cc_final: 0.7726 (t80) outliers start: 42 outliers final: 30 residues processed: 243 average time/residue: 0.4878 time to fit residues: 163.9282 Evaluate side-chains 223 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS 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 D residue 66 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 46 LEU 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 80 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.095938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.072058 restraints weight = 385874.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.074820 restraints weight = 194413.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.076589 restraints weight = 120673.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.077728 restraints weight = 86004.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.078478 restraints weight = 67738.740| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25202 Z= 0.229 Angle : 0.667 5.845 36484 Z= 0.416 Chirality : 0.043 0.161 4144 Planarity : 0.005 0.049 2636 Dihedral : 30.166 89.741 7918 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.66 % Allowed : 16.18 % Favored : 81.16 % 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 (0.21), residues: 1472 helix: 1.23 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 21 TYR 0.021 0.002 TYR F 73 PHE 0.011 0.002 PHE D 66 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00478 (25202) covalent geometry : angle 0.66727 (36484) hydrogen bonds : bond 0.08285 ( 1476) hydrogen bonds : angle 3.79023 ( 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 231 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.880 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: A 130 ARG cc_start: 0.8701 (mmp-170) cc_final: 0.8470 (mmm160) REVERT: C 69 ASN cc_start: 0.7813 (m-40) cc_final: 0.7523 (m-40) REVERT: D 106 GLU cc_start: 0.9403 (mp0) cc_final: 0.8775 (pm20) REVERT: G 96 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8810 (tmtt) REVERT: L 68 PHE cc_start: 0.7716 (t80) cc_final: 0.7380 (t80) REVERT: N 62 GLU cc_start: 0.9389 (tp30) cc_final: 0.9070 (tm-30) REVERT: P 91 MET cc_start: 0.9502 (tpp) cc_final: 0.9275 (tpp) REVERT: P 100 TYR cc_start: 0.7979 (t80) cc_final: 0.7349 (t80) outliers start: 33 outliers final: 28 residues processed: 222 average time/residue: 0.4247 time to fit residues: 132.1996 Evaluate side-chains 216 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 63 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 93 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 63 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 110 HIS ** 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 85 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 = 0.4701 r_free = 0.4701 target = 0.091262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.068154 restraints weight = 412216.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.070552 restraints weight = 219642.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.072059 restraints weight = 139502.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.073090 restraints weight = 101971.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.073773 restraints weight = 81636.484| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25202 Z= 0.264 Angle : 0.708 7.339 36484 Z= 0.437 Chirality : 0.044 0.186 4144 Planarity : 0.006 0.059 2636 Dihedral : 30.484 89.990 7918 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.30 % Allowed : 15.86 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1472 helix: 0.87 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 80 TYR 0.025 0.002 TYR P 100 PHE 0.022 0.003 PHE Q 62 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00552 (25202) covalent geometry : angle 0.70803 (36484) hydrogen bonds : bond 0.09477 ( 1476) hydrogen bonds : angle 4.12708 ( 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 236 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.866 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: A 130 ARG cc_start: 0.8531 (mmp-170) cc_final: 0.8286 (mmm160) REVERT: D 106 GLU cc_start: 0.9433 (mp0) cc_final: 0.8939 (pm20) REVERT: G 96 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8864 (tmtt) REVERT: L 68 PHE cc_start: 0.7932 (t80) cc_final: 0.7569 (t80) REVERT: M 68 ARG cc_start: 0.9154 (ttm110) cc_final: 0.8842 (ttp-110) REVERT: N 62 GLU cc_start: 0.9437 (tp30) cc_final: 0.9174 (tm-30) REVERT: P 100 TYR cc_start: 0.8180 (t80) cc_final: 0.7893 (t80) REVERT: R 95 ASN cc_start: 0.7927 (t0) cc_final: 0.7563 (m-40) outliers start: 41 outliers final: 35 residues processed: 223 average time/residue: 0.4163 time to fit residues: 130.7579 Evaluate side-chains 219 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 64 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 C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 GLU 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 P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** L 94 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 = 0.4705 r_free = 0.4705 target = 0.091259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.068124 restraints weight = 412021.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.070576 restraints weight = 213230.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.072071 restraints weight = 134684.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.073100 restraints weight = 98576.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.073779 restraints weight = 79090.111| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.8479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25202 Z= 0.230 Angle : 0.671 8.022 36484 Z= 0.417 Chirality : 0.042 0.159 4144 Planarity : 0.005 0.064 2636 Dihedral : 30.552 89.118 7918 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 17.55 % Favored : 79.63 % 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: 1.08 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.019 0.002 TYR F 73 PHE 0.012 0.002 PHE D 66 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00478 (25202) covalent geometry : angle 0.67115 (36484) hydrogen bonds : bond 0.08165 ( 1476) hydrogen bonds : angle 3.92922 ( 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 233 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.909 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: A 130 ARG cc_start: 0.8275 (mmp-170) cc_final: 0.8037 (mmm160) REVERT: C 69 ASN cc_start: 0.7746 (m-40) cc_final: 0.7444 (m-40) REVERT: D 106 GLU cc_start: 0.9279 (mp0) cc_final: 0.8799 (pm20) REVERT: G 96 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8894 (tmtt) REVERT: L 68 PHE cc_start: 0.7971 (t80) cc_final: 0.7609 (t80) REVERT: N 62 GLU cc_start: 0.9425 (tp30) cc_final: 0.9191 (tm-30) REVERT: O 36 GLU cc_start: 0.2941 (OUTLIER) cc_final: 0.0853 (tm-30) REVERT: P 100 TYR cc_start: 0.8052 (t80) cc_final: 0.7719 (t80) REVERT: R 95 ASN cc_start: 0.7990 (t0) cc_final: 0.7635 (m-40) outliers start: 35 outliers final: 30 residues processed: 224 average time/residue: 0.4022 time to fit residues: 126.9845 Evaluate side-chains 215 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 80 ARG 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: 10.0000 chunk 13 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN G 111 ASN G 113 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 HIS ** S 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 85 ASN ** 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 = 0.4670 r_free = 0.4670 target = 0.088104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.065196 restraints weight = 422449.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.067532 restraints weight = 217916.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.069004 restraints weight = 138372.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.069950 restraints weight = 100485.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.070594 restraints weight = 80937.556| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 25202 Z= 0.274 Angle : 0.701 6.593 36484 Z= 0.436 Chirality : 0.045 0.166 4144 Planarity : 0.006 0.094 2636 Dihedral : 30.755 89.992 7918 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.54 % Allowed : 18.60 % Favored : 77.86 % 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: 0.23 (0.21), residues: 1472 helix: 0.80 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 68 TYR 0.022 0.002 TYR H 122 PHE 0.011 0.002 PHE H 66 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00571 (25202) covalent geometry : angle 0.70140 (36484) hydrogen bonds : bond 0.10327 ( 1476) hydrogen bonds : angle 4.22658 ( 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 235 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.945 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: A 130 ARG cc_start: 0.8268 (mmp-170) cc_final: 0.8012 (mmm160) REVERT: D 106 GLU cc_start: 0.9346 (mp0) cc_final: 0.8944 (pm20) REVERT: F 99 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.5715 (m-10) REVERT: G 42 GLU cc_start: 0.7707 (pt0) cc_final: 0.7390 (tm-30) REVERT: G 96 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8946 (tmtt) REVERT: L 68 PHE cc_start: 0.8079 (t80) cc_final: 0.7754 (t80) REVERT: P 100 TYR cc_start: 0.8103 (t80) cc_final: 0.7717 (t80) REVERT: R 95 ASN cc_start: 0.8096 (t0) cc_final: 0.7788 (m-40) outliers start: 44 outliers final: 41 residues processed: 221 average time/residue: 0.4549 time to fit residues: 142.1303 Evaluate side-chains 226 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 64 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 C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain S residue 80 ARG 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: 0.6980 chunk 133 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 113 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.117557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.087584 restraints weight = 475302.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.089639 restraints weight = 265783.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.090981 restraints weight = 176003.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.091739 restraints weight = 133492.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.092307 restraints weight = 111993.060| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.9685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25202 Z= 0.243 Angle : 0.682 7.105 36484 Z= 0.424 Chirality : 0.042 0.155 4144 Planarity : 0.005 0.102 2636 Dihedral : 30.894 89.695 7918 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.98 % Allowed : 19.65 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1472 helix: 0.93 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -1.43 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 117 TYR 0.018 0.002 TYR F 73 PHE 0.012 0.002 PHE D 66 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00504 (25202) covalent geometry : angle 0.68228 (36484) hydrogen bonds : bond 0.08640 ( 1476) hydrogen bonds : angle 4.08890 ( 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 227 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.826 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: D 106 GLU cc_start: 0.9214 (mp0) cc_final: 0.8844 (pm20) REVERT: G 42 GLU cc_start: 0.7775 (pt0) cc_final: 0.7382 (tm-30) REVERT: L 68 PHE cc_start: 0.8291 (t80) cc_final: 0.7999 (t80) REVERT: P 82 ASP cc_start: 0.9137 (p0) cc_final: 0.8924 (t0) REVERT: P 100 TYR cc_start: 0.8016 (t80) cc_final: 0.7592 (t80) REVERT: R 95 ASN cc_start: 0.7722 (t0) cc_final: 0.7437 (m-40) outliers start: 37 outliers final: 33 residues processed: 216 average time/residue: 0.4309 time to fit residues: 132.0949 Evaluate side-chains 217 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 96 GLN 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: 0.8980 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.116261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.086363 restraints weight = 478427.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.088418 restraints weight = 266819.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.089715 restraints weight = 177624.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.090565 restraints weight = 134791.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.091088 restraints weight = 112130.865| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25202 Z= 0.253 Angle : 0.687 7.167 36484 Z= 0.427 Chirality : 0.043 0.159 4144 Planarity : 0.006 0.123 2636 Dihedral : 30.907 89.065 7918 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.58 % Allowed : 20.77 % Favored : 76.65 % 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 (0.21), residues: 1472 helix: 0.88 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.017 0.002 TYR F 73 PHE 0.011 0.002 PHE H 66 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00525 (25202) covalent geometry : angle 0.68701 (36484) hydrogen bonds : bond 0.09543 ( 1476) hydrogen bonds : angle 4.17263 ( 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 215 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.757 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: D 106 GLU cc_start: 0.9205 (mp0) cc_final: 0.8895 (pm20) REVERT: F 99 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.5782 (m-10) REVERT: G 42 GLU cc_start: 0.7871 (pt0) cc_final: 0.7422 (tm-30) REVERT: L 106 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9220 (mm-30) REVERT: M 54 GLU cc_start: 0.7683 (tt0) cc_final: 0.7367 (pt0) REVERT: P 100 TYR cc_start: 0.8074 (t80) cc_final: 0.7669 (t80) outliers start: 32 outliers final: 29 residues processed: 207 average time/residue: 0.4387 time to fit residues: 128.4944 Evaluate side-chains 212 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 96 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.084257 restraints weight = 487849.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.086253 restraints weight = 273868.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.087514 restraints weight = 183641.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.088284 restraints weight = 139326.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.088856 restraints weight = 116605.174| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 1.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25202 Z= 0.281 Angle : 0.726 8.939 36484 Z= 0.448 Chirality : 0.045 0.160 4144 Planarity : 0.007 0.215 2636 Dihedral : 31.215 92.064 7918 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.74 % Allowed : 20.85 % Favored : 76.41 % 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: -0.21 (0.21), residues: 1472 helix: 0.49 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 64 TYR 0.017 0.002 TYR F 73 PHE 0.012 0.002 PHE D 66 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00584 (25202) covalent geometry : angle 0.72562 (36484) hydrogen bonds : bond 0.10427 ( 1476) hydrogen bonds : angle 4.41415 ( 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 219 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.887 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: D 106 GLU cc_start: 0.9235 (mp0) cc_final: 0.8867 (pm20) REVERT: F 99 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: G 42 GLU cc_start: 0.7986 (pt0) cc_final: 0.7427 (tm-30) REVERT: H 63 MET cc_start: 0.7149 (mmp) cc_final: 0.6931 (mmp) REVERT: H 93 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7294 (mpp-170) REVERT: L 106 GLU cc_start: 0.9605 (tm-30) cc_final: 0.9286 (mm-30) REVERT: N 88 ILE cc_start: 0.5896 (mt) cc_final: 0.5548 (tp) REVERT: P 100 TYR cc_start: 0.8075 (t80) cc_final: 0.7594 (t80) outliers start: 34 outliers final: 32 residues processed: 210 average time/residue: 0.4540 time to fit residues: 133.7290 Evaluate side-chains 213 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 50 HIS 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 M residue 92 LYS Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 96 GLN 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: 20.0000 chunk 22 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 157 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 113 GLN H 64 ASN ** L 94 GLN ** 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 = 0.5016 r_free = 0.5016 target = 0.117540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.088098 restraints weight = 480811.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.090244 restraints weight = 266240.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.091594 restraints weight = 174709.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.092312 restraints weight = 131076.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.092963 restraints weight = 110606.266| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 1.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25202 Z= 0.191 Angle : 0.661 7.162 36484 Z= 0.410 Chirality : 0.039 0.145 4144 Planarity : 0.005 0.087 2636 Dihedral : 31.000 93.631 7918 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.42 % Allowed : 21.18 % Favored : 76.41 % 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: 0.71 (0.22), residues: 1472 helix: 1.22 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 64 TYR 0.019 0.001 TYR E 100 PHE 0.012 0.001 PHE D 66 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00404 (25202) covalent geometry : angle 0.66083 (36484) hydrogen bonds : bond 0.06716 ( 1476) hydrogen bonds : angle 3.79466 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12689.04 seconds wall clock time: 215 minutes 16.49 seconds (12916.49 seconds total)