Starting phenix.real_space_refine on Mon Aug 10 05:54:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmm_48394/08_2026/9mmm_48394.map" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 570 5.49 5 S 28 5.16 5 C 13060 2.51 5 N 4428 2.21 5 O 5526 1.98 5 H 18934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "N" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "R" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "X" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "Y" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 6.63, per 1000 atoms: 0.16 Number of scatterers: 42546 At special positions: 0 Unit cell: (123.97, 127.05, 148.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 570 15.00 O 5526 8.00 N 4428 7.00 C 13060 6.00 H 18934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 987.9 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 20 sheets defined 72.2% alpha, 2.9% beta 282 base pairs and 524 stacking pairs defined. Time for finding SS restraints: 7.49 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.546A pdb=" N GLN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.864A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.515A pdb=" N GLY B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.864A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.555A 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: 3.668A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.140A 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: 3.836A 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: 3.750A 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: 3.639A 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: 3.510A 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: 3.660A 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: 3.702A 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: 3.547A pdb=" N GLN L 77 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 114 removed outlier: 3.864A pdb=" N VAL L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.660A 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: 3.710A pdb=" N GLU M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.743A 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: 3.649A 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: 3.746A 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: 3.814A pdb=" N SER O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 58 removed outlier: 3.570A 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: 3.863A pdb=" N VAL P 90 " --> pdb=" O GLN P 86 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 3.783A 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: 3.668A pdb=" N ILE P 125 " --> pdb=" O MET P 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 30 removed outlier: 4.139A 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: 3.835A pdb=" N GLU Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.641A 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: 3.511A 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: 3.658A pdb=" N LYS S 109 " --> pdb=" O GLY S 105 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.525A 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: 6.953A 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: 3.526A 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: 7.099A pdb=" N ARG N 43 " --> pdb=" O ILE O 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'N' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'P' and resid 84 through 85 removed outlier: 6.953A pdb=" N ARG P 84 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'P' and resid 119 through 120 Processing sheet with id=AC1, first strand: chain 'R' and resid 43 through 44 removed outlier: 7.219A pdb=" N ARG R 43 " --> pdb=" O ILE S 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'R' and resid 78 through 79 752 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 724 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 282 basepair parallelities 524 stacking parallelities Total time for adding SS restraints: 10.21 Time building geometry restraints manager: 5.07 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 - 1.22: 195 1.22 - 1.42: 10717 1.42 - 1.61: 14250 1.61 - 1.81: 48 Bond restraints: 44136 Sorted by residual: bond pdb=" C3' DC X 69 " pdb=" C2' DC X 69 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.43e+01 bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.40e+01 bond pdb=" C3' DA I -5 " pdb=" C2' DA I -5 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.24e+01 bond pdb=" C3' DA X -5 " pdb=" C2' DA X -5 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.17e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.94e+01 ... (remaining 44131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 69431 1.32 - 2.65: 9350 2.65 - 3.97: 950 3.97 - 5.30: 259 5.30 - 6.62: 14 Bond angle restraints: 80004 Sorted by residual: angle pdb=" O4' DC X 66 " pdb=" C1' DC X 66 " pdb=" N1 DC X 66 " ideal model delta sigma weight residual 108.00 113.19 -5.19 7.00e-01 2.04e+00 5.50e+01 angle pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " pdb=" N1 DC I 66 " ideal model delta sigma weight residual 108.00 113.14 -5.14 7.00e-01 2.04e+00 5.39e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 112.96 -4.96 7.00e-01 2.04e+00 5.01e+01 angle pdb=" O4' DG Y 27 " pdb=" C1' DG Y 27 " pdb=" N9 DG Y 27 " ideal model delta sigma weight residual 108.00 112.92 -4.92 7.00e-01 2.04e+00 4.94e+01 angle pdb=" O4' DT I 34 " pdb=" C1' DT I 34 " pdb=" N1 DT I 34 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.99e+01 ... (remaining 79999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 12853 17.19 - 34.38: 2403 34.38 - 51.57: 1837 51.57 - 68.76: 1209 68.76 - 85.95: 26 Dihedral angle restraints: 18328 sinusoidal: 13456 harmonic: 4872 Sorted by residual: 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 -43.87 -46.13 2 1.50e+01 4.44e-03 1.11e+01 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 -43.88 -46.12 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 180.00 135.61 44.39 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 18325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2298 0.043 - 0.085: 1112 0.085 - 0.128: 514 0.128 - 0.170: 192 0.170 - 0.213: 28 Chirality restraints: 4144 Sorted by residual: chirality pdb=" C4' DC I 69 " pdb=" C5' DC I 69 " pdb=" O4' DC I 69 " pdb=" C3' DC I 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C4' DC X 69 " pdb=" C5' DC X 69 " pdb=" O4' DC X 69 " pdb=" C3' DC X 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4141 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " 0.024 9.50e-02 1.11e+02 3.95e-02 3.37e+01 pdb=" NE ARG C 33 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.031 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 " 0.002 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 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 33 " -0.023 9.50e-02 1.11e+02 3.93e-02 3.36e+01 pdb=" NE ARG N 33 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG N 33 " -0.032 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 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG N 33 " 0.073 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 H 87 " 0.409 9.50e-02 1.11e+02 1.39e-01 3.30e+01 pdb=" NE ARG H 87 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG H 87 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 87 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG H 87 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG H 87 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 87 " 0.019 2.00e-02 2.50e+03 pdb="HH21 ARG H 87 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 87 " 0.046 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1191 2.19 - 2.79: 69352 2.79 - 3.39: 99139 3.39 - 4.00: 140985 4.00 - 4.60: 223275 Nonbonded interactions: 533942 Sorted by model distance: nonbonded pdb=" OE1 GLU P 74 " pdb="HD21 ASN Q 26 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU E 74 " pdb="HD21 ASN F 26 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP P 107 " pdb="HH11 ARG P 132 " model vdw 1.602 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP D 69 " pdb=" HH TYR F 99 " model vdw 1.611 2.450 ... (remaining 533937 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 42.810 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 25202 Z= 0.618 Angle : 1.019 6.621 36484 Z= 0.862 Chirality : 0.062 0.213 4144 Planarity : 0.013 0.152 2636 Dihedral : 26.173 85.946 10870 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.88 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: 0.45 (0.14), residues: 1062 sheet: None (None), residues: 0 loop : -0.32 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG P 64 TYR 0.020 0.005 TYR G 58 PHE 0.017 0.003 PHE D 66 HIS 0.012 0.003 HIS O 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.62 (25202) covalent geometry : angle 1.01903 / 0.86 (36484) hydrogen bonds : bond 0.13253 / 8.99 ( 1476) hydrogen bonds : angle 3.78032 / 2.75 ( 3662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 507 time to evaluate : 0.933 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 63 ILE cc_start: 0.7512 (mt) cc_final: 0.7302 (mm) REVERT: B 44 VAL cc_start: 0.7417 (t) cc_final: 0.6035 (t) REVERT: B 73 TYR cc_start: 0.8166 (m-80) cc_final: 0.7691 (t80) REVERT: E 49 LEU cc_start: 0.9383 (mt) cc_final: 0.9182 (mm) REVERT: E 52 ILE cc_start: 0.9402 (mt) cc_final: 0.9185 (mm) REVERT: F 58 VAL cc_start: 0.8904 (t) cc_final: 0.8452 (m) REVERT: G 69 ASN cc_start: 0.9027 (m-40) cc_final: 0.8324 (m110) REVERT: H 116 THR cc_start: 0.9130 (p) cc_final: 0.8825 (p) REVERT: M 82 VAL cc_start: 0.5764 (t) cc_final: 0.5516 (t) REVERT: O 42 VAL cc_start: 0.7602 (t) cc_final: 0.7329 (t) REVERT: O 97 THR cc_start: 0.8984 (m) cc_final: 0.8727 (p) REVERT: R 69 ASN cc_start: 0.8809 (m-40) cc_final: 0.8272 (t0) outliers start: 2 outliers final: 1 residues processed: 507 average time/residue: 0.4528 time to fit residues: 325.0692 Evaluate side-chains 318 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 93 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN D 96 GLN M 26 ASN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN S 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.113385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.097240 restraints weight = 524902.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.099372 restraints weight = 342264.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.100835 restraints weight = 247626.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.101912 restraints weight = 194466.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.102714 restraints weight = 161080.810| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25202 Z= 0.260 Angle : 0.826 9.539 36484 Z= 0.504 Chirality : 0.051 0.189 4144 Planarity : 0.007 0.097 2636 Dihedral : 29.464 85.771 7922 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.42 % Allowed : 12.88 % Favored : 84.70 % 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: 0.43 (0.20), residues: 1472 helix: 0.76 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 100 TYR 0.019 0.002 TYR O 43 PHE 0.018 0.002 PHE P 68 HIS 0.014 0.002 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.26 (25202) covalent geometry : angle 0.82594 / 0.50 (36484) hydrogen bonds : bond 0.10348 / 6.87 ( 1476) hydrogen bonds : angle 4.17676 / 3.07 ( 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 354 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 0.829 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8857 (m-80) cc_final: 0.8214 (t80) REVERT: C 65 GLU cc_start: 0.9343 (tt0) cc_final: 0.9013 (tp30) REVERT: G 69 ASN cc_start: 0.9300 (m-40) cc_final: 0.8915 (m110) REVERT: M 82 VAL cc_start: 0.6577 (t) cc_final: 0.6348 (t) REVERT: P 79 PHE cc_start: 0.8146 (t80) cc_final: 0.7743 (t80) REVERT: R 69 ASN cc_start: 0.8757 (m-40) cc_final: 0.8536 (t0) REVERT: S 36 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6873 (tp30) outliers start: 30 outliers final: 20 residues processed: 343 average time/residue: 0.4122 time to fit residues: 203.6454 Evaluate side-chains 302 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 183 optimal weight: 40.0000 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** O 96 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 = 0.4634 r_free = 0.4634 target = 0.110996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.094779 restraints weight = 530031.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.096864 restraints weight = 345022.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.098303 restraints weight = 249466.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.099346 restraints weight = 196027.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.100102 restraints weight = 162679.215| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25202 Z= 0.189 Angle : 0.666 8.128 36484 Z= 0.440 Chirality : 0.043 0.174 4144 Planarity : 0.005 0.061 2636 Dihedral : 29.837 87.531 7918 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.25 % Allowed : 15.22 % Favored : 82.53 % 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: 0.85 (0.20), residues: 1472 helix: 1.12 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 130 TYR 0.022 0.002 TYR M 89 PHE 0.024 0.002 PHE F 101 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.19 (25202) covalent geometry : angle 0.66629 / 0.44 (36484) hydrogen bonds : bond 0.07895 / 5.24 ( 1476) hydrogen bonds : angle 3.78161 / 2.77 ( 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 325 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.920 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: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.9346 (tt0) cc_final: 0.8953 (tp30) REVERT: G 69 ASN cc_start: 0.9243 (m-40) cc_final: 0.8852 (m110) REVERT: M 82 VAL cc_start: 0.6433 (t) cc_final: 0.6195 (t) REVERT: R 62 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9022 (tp30) REVERT: R 69 ASN cc_start: 0.8800 (m-40) cc_final: 0.8585 (t0) outliers start: 28 outliers final: 25 residues processed: 315 average time/residue: 0.4248 time to fit residues: 193.5888 Evaluate side-chains 296 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain L residue 68 PHE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 195 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 overall best weight: 7.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.105405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.089423 restraints weight = 543945.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.091431 restraints weight = 355058.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.092785 restraints weight = 257025.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.093797 restraints weight = 202580.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.094391 restraints weight = 168283.159| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 25202 Z= 0.240 Angle : 0.724 8.099 36484 Z= 0.459 Chirality : 0.046 0.185 4144 Planarity : 0.005 0.036 2636 Dihedral : 30.208 89.110 7918 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.14 % Allowed : 16.02 % 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: 0.09 (0.20), residues: 1472 helix: 0.59 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 30 TYR 0.029 0.002 TYR Q 73 PHE 0.013 0.002 PHE A 68 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.24 (25202) covalent geometry : angle 0.72418 / 0.46 (36484) hydrogen bonds : bond 0.10886 / 7.15 ( 1476) hydrogen bonds : angle 4.17063 / 3.04 ( 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 317 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.730 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: B 73 TYR cc_start: 0.8869 (m-80) cc_final: 0.7982 (m-80) REVERT: C 65 GLU cc_start: 0.9379 (tt0) cc_final: 0.9006 (tp30) REVERT: D 60 MET cc_start: 0.8356 (tpp) cc_final: 0.8072 (tpt) REVERT: M 82 VAL cc_start: 0.6423 (t) cc_final: 0.6178 (t) REVERT: M 85 MET cc_start: 0.7111 (ppp) cc_final: 0.6885 (ppp) REVERT: R 58 TYR cc_start: 0.8822 (t80) cc_final: 0.8567 (t80) outliers start: 39 outliers final: 35 residues processed: 305 average time/residue: 0.3867 time to fit residues: 170.5771 Evaluate side-chains 296 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN P 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.107274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.091108 restraints weight = 543294.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.093209 restraints weight = 356701.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.094628 restraints weight = 256407.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.095647 restraints weight = 200674.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.096381 restraints weight = 166639.710| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25202 Z= 0.155 Angle : 0.638 6.709 36484 Z= 0.415 Chirality : 0.043 0.169 4144 Planarity : 0.005 0.087 2636 Dihedral : 30.363 89.504 7918 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.42 % Allowed : 17.55 % Favored : 80.03 % 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: 0.96 (0.20), residues: 1472 helix: 1.26 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 80 TYR 0.014 0.002 TYR Q 73 PHE 0.013 0.001 PHE D 66 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.16 (25202) covalent geometry : angle 0.63792 / 0.42 (36484) hydrogen bonds : bond 0.06347 / 4.16 ( 1476) hydrogen bonds : angle 3.65131 / 2.66 ( 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 308 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 0.875 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: D 60 MET cc_start: 0.8248 (tpp) cc_final: 0.7845 (tpt) REVERT: G 69 ASN cc_start: 0.9314 (m-40) cc_final: 0.8653 (m110) REVERT: M 82 VAL cc_start: 0.6305 (t) cc_final: 0.6063 (t) REVERT: R 36 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6842 (ttm170) outliers start: 30 outliers final: 26 residues processed: 299 average time/residue: 0.4055 time to fit residues: 174.7802 Evaluate side-chains 290 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 117 LYS Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 178 optimal weight: 40.0000 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 114 HIS P 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.102766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.086873 restraints weight = 555491.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.088808 restraints weight = 362264.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.090135 restraints weight = 263335.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.091047 restraints weight = 207576.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.091694 restraints weight = 174341.475| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 25202 Z= 0.233 Angle : 0.689 7.036 36484 Z= 0.440 Chirality : 0.043 0.182 4144 Planarity : 0.005 0.042 2636 Dihedral : 30.467 88.734 7918 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.22 % Allowed : 17.79 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1472 helix: 0.83 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.014 0.002 TYR Q 73 PHE 0.011 0.002 PHE F 101 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.23 (25202) covalent geometry : angle 0.68912 / 0.44 (36484) hydrogen bonds : bond 0.10280 / 6.72 ( 1476) hydrogen bonds : angle 4.13339 / 3.00 ( 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 292 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 60 MET cc_start: 0.8291 (tpp) cc_final: 0.7968 (tpt) REVERT: G 51 TYR cc_start: 0.8922 (m-80) cc_final: 0.8353 (m-80) REVERT: G 69 ASN cc_start: 0.9040 (m-40) cc_final: 0.8742 (m110) REVERT: M 85 MET cc_start: 0.7103 (ppp) cc_final: 0.6891 (ppp) REVERT: R 36 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6797 (ttm170) outliers start: 40 outliers final: 35 residues processed: 279 average time/residue: 0.4080 time to fit residues: 164.3646 Evaluate side-chains 276 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 117 LYS Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 197 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 190 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS O 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.101235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.085459 restraints weight = 556145.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.087358 restraints weight = 364004.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.088711 restraints weight = 264639.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.089571 restraints weight = 208104.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.090109 restraints weight = 175518.414| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 25202 Z= 0.212 Angle : 0.677 6.875 36484 Z= 0.434 Chirality : 0.043 0.201 4144 Planarity : 0.005 0.057 2636 Dihedral : 30.676 88.477 7918 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.98 % Allowed : 18.76 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1472 helix: 0.77 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 79 TYR 0.017 0.002 TYR H 43 PHE 0.012 0.002 PHE L 68 HIS 0.009 0.001 HIS S 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.21 (25202) covalent geometry : angle 0.67748 / 0.43 (36484) hydrogen bonds : bond 0.09337 / 6.10 ( 1476) hydrogen bonds : angle 4.15628 / 3.02 ( 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 278 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.038 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: D 60 MET cc_start: 0.8296 (tpp) cc_final: 0.7964 (tpt) REVERT: G 51 TYR cc_start: 0.8928 (m-80) cc_final: 0.8339 (m-80) REVERT: G 69 ASN cc_start: 0.9060 (m-40) cc_final: 0.8734 (m110) REVERT: L 105 PHE cc_start: 0.9653 (m-80) cc_final: 0.9326 (m-10) REVERT: R 36 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6860 (ttm170) outliers start: 37 outliers final: 33 residues processed: 263 average time/residue: 0.4136 time to fit residues: 158.0850 Evaluate side-chains 270 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 LEU 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 C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 117 LYS Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 95 ASN Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 192 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 0.9990 chunk 174 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 113 optimal weight: 0.0270 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN P 69 GLN P 109 ASN P 114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.102598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.086742 restraints weight = 551270.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.088650 restraints weight = 359310.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.090064 restraints weight = 260955.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.090940 restraints weight = 204377.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.091595 restraints weight = 171884.718| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25202 Z= 0.158 Angle : 0.646 7.364 36484 Z= 0.416 Chirality : 0.042 0.214 4144 Planarity : 0.004 0.046 2636 Dihedral : 30.703 86.434 7918 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.50 % Allowed : 19.48 % Favored : 78.02 % 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: 0.91 (0.21), residues: 1472 helix: 1.26 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 43 TYR 0.014 0.002 TYR H 41 PHE 0.009 0.001 PHE H 66 HIS 0.026 0.001 HIS L 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.16 (25202) covalent geometry : angle 0.64585 / 0.42 (36484) hydrogen bonds : bond 0.07122 / 4.65 ( 1476) hydrogen bonds : angle 3.81860 / 2.77 ( 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 276 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.822 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: D 60 MET cc_start: 0.8249 (tpp) cc_final: 0.7905 (tpt) REVERT: G 51 TYR cc_start: 0.8934 (m-80) cc_final: 0.8354 (m-80) REVERT: G 69 ASN cc_start: 0.9052 (m-40) cc_final: 0.8734 (m110) REVERT: L 105 PHE cc_start: 0.9652 (m-80) cc_final: 0.9282 (m-10) REVERT: M 54 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: R 36 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6855 (ttm170) outliers start: 31 outliers final: 27 residues processed: 266 average time/residue: 0.4159 time to fit residues: 160.3417 Evaluate side-chains 269 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.101258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.085492 restraints weight = 555946.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.087420 restraints weight = 361966.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.088758 restraints weight = 262978.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.089653 restraints weight = 206703.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.090145 restraints weight = 173959.657| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 25202 Z= 0.187 Angle : 0.657 7.400 36484 Z= 0.420 Chirality : 0.042 0.193 4144 Planarity : 0.005 0.043 2636 Dihedral : 30.720 85.993 7918 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 2.66 % Allowed : 19.40 % Favored : 77.94 % 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: 0.79 (0.21), residues: 1472 helix: 1.16 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 89 TYR 0.013 0.002 TYR H 41 PHE 0.019 0.001 PHE B 62 HIS 0.021 0.001 HIS L 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.19 (25202) covalent geometry : angle 0.65663 / 0.42 (36484) hydrogen bonds : bond 0.08161 / 5.33 ( 1476) hydrogen bonds : angle 3.94854 / 2.87 ( 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 273 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.897 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: G 51 TYR cc_start: 0.8982 (m-80) cc_final: 0.8383 (m-80) REVERT: G 69 ASN cc_start: 0.9064 (m-40) cc_final: 0.8809 (m110) REVERT: L 105 PHE cc_start: 0.9662 (m-80) cc_final: 0.9292 (m-10) REVERT: M 54 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8628 (pt0) REVERT: R 36 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6833 (ttm170) outliers start: 33 outliers final: 28 residues processed: 260 average time/residue: 0.4291 time to fit residues: 162.6822 Evaluate side-chains 265 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 175 optimal weight: 30.0000 chunk 170 optimal weight: 40.0000 chunk 176 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.101314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.085544 restraints weight = 555871.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.087476 restraints weight = 361997.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.088790 restraints weight = 262535.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.089676 restraints weight = 206959.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.090270 restraints weight = 174580.500| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.265 25202 Z= 0.215 Angle : 0.762 59.200 36484 Z= 0.487 Chirality : 0.042 0.218 4144 Planarity : 0.005 0.043 2636 Dihedral : 30.722 86.021 7918 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 2.50 % Allowed : 19.73 % Favored : 77.78 % Cbeta Deviations : 0.07 % 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: 0.78 (0.21), residues: 1472 helix: 1.16 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.013 0.002 TYR H 41 PHE 0.019 0.001 PHE B 62 HIS 0.011 0.001 HIS L 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.21 (25202) covalent geometry : angle 0.76222 / 0.49 (36484) hydrogen bonds : bond 0.08145 / 5.32 ( 1476) hydrogen bonds : angle 3.94695 / 2.87 ( 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 266 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.971 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: G 51 TYR cc_start: 0.8981 (m-80) cc_final: 0.8380 (m-80) REVERT: G 69 ASN cc_start: 0.9086 (m-40) cc_final: 0.8808 (m110) REVERT: L 105 PHE cc_start: 0.9663 (m-80) cc_final: 0.9296 (m-10) REVERT: M 54 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8633 (pt0) REVERT: R 36 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6827 (ttm170) outliers start: 31 outliers final: 29 residues processed: 255 average time/residue: 0.4332 time to fit residues: 161.5522 Evaluate side-chains 264 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.101311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.085477 restraints weight = 559639.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.087367 restraints weight = 366311.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.088738 restraints weight = 267161.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.089612 restraints weight = 209602.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.090141 restraints weight = 176612.596| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.265 25202 Z= 0.215 Angle : 0.762 59.200 36484 Z= 0.487 Chirality : 0.042 0.218 4144 Planarity : 0.005 0.043 2636 Dihedral : 30.722 86.021 7918 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 2.50 % Allowed : 19.73 % Favored : 77.78 % Cbeta Deviations : 0.07 % 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: 0.78 (0.21), residues: 1472 helix: 1.16 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.013 0.002 TYR H 41 PHE 0.019 0.001 PHE B 62 HIS 0.011 0.001 HIS L 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.21 (25202) covalent geometry : angle 0.76222 / 0.49 (36484) hydrogen bonds : bond 0.08145 / 5.32 ( 1476) hydrogen bonds : angle 3.94695 / 2.87 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9816.65 seconds wall clock time: 167 minutes 4.24 seconds (10024.24 seconds total)