Starting phenix.real_space_refine on Tue Jul 7 03:48:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmm_48394/07_2026/9mmm_48394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmm_48394/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmm_48394/07_2026/9mmm_48394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmm_48394/07_2026/9mmm_48394.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmm_48394/07_2026/9mmm_48394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmm_48394/07_2026/9mmm_48394.cif" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "N" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "R" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "X" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "Y" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 5.43, per 1000 atoms: 0.13 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: 2.97 Conformation dependent library (CDL) restraints added in 942.8 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: 7.84 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: 10.70 Time building geometry restraints manager: 4.20 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: 69575 1.32 - 2.65: 9265 2.65 - 3.97: 893 3.97 - 5.30: 257 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: 5.230 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: 0.220 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 41.280 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- 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 : 1.006 6.621 36484 Z= 0.847 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 1.00565 / 0.85 (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 : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7301 (mm) REVERT: B 44 VAL cc_start: 0.7417 (t) cc_final: 0.6036 (t) REVERT: B 73 TYR cc_start: 0.8166 (m-80) cc_final: 0.7691 (t80) REVERT: E 52 ILE cc_start: 0.9402 (mt) cc_final: 0.9186 (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: 0.5515 (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: 0.4088 time to fit residues: 292.6832 Evaluate side-chains 313 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 = 0.4679 r_free = 0.4679 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.098003 restraints weight = 523016.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.100201 restraints weight = 342602.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.101664 restraints weight = 246660.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.102650 restraints weight = 193152.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.103470 restraints weight = 162416.133| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25202 Z= 0.245 Angle : 0.791 8.890 36484 Z= 0.494 Chirality : 0.049 0.179 4144 Planarity : 0.006 0.089 2636 Dihedral : 29.366 84.817 7922 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.50 % Allowed : 13.53 % Favored : 83.98 % 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: 0.74 (0.20), residues: 1472 helix: 1.00 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.76 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 100 TYR 0.018 0.002 TYR O 43 PHE 0.016 0.002 PHE P 68 HIS 0.013 0.002 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.25 (25202) covalent geometry : angle 0.79087 / 0.49 (36484) hydrogen bonds : bond 0.09855 / 6.55 ( 1476) hydrogen bonds : angle 4.04162 / 2.98 ( 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 353 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 0.682 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: B 73 TYR cc_start: 0.8835 (m-80) cc_final: 0.8176 (t80) REVERT: C 65 GLU cc_start: 0.9330 (tt0) cc_final: 0.9000 (tp30) REVERT: G 69 ASN cc_start: 0.9284 (m-40) cc_final: 0.8873 (m110) REVERT: M 82 VAL cc_start: 0.6610 (t) cc_final: 0.6384 (t) REVERT: P 79 PHE cc_start: 0.8117 (t80) cc_final: 0.7732 (t80) REVERT: R 69 ASN cc_start: 0.8736 (m-40) cc_final: 0.8526 (t0) outliers start: 31 outliers final: 21 residues processed: 341 average time/residue: 0.3948 time to fit residues: 193.2298 Evaluate side-chains 304 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 77 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain N residue 65 GLU 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 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 164 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 overall best weight: 5.6390 ------------------------------------------------------------------------------- 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 = 0.4637 r_free = 0.4637 target = 0.111208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.094941 restraints weight = 529729.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.097015 restraints weight = 345313.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.098469 restraints weight = 250630.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.099502 restraints weight = 196303.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.100269 restraints weight = 163467.029| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25202 Z= 0.194 Angle : 0.666 8.267 36484 Z= 0.441 Chirality : 0.043 0.207 4144 Planarity : 0.006 0.075 2636 Dihedral : 29.810 87.296 7918 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.33 % Allowed : 15.62 % Favored : 82.05 % 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: 0.86 (0.20), residues: 1472 helix: 1.13 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 93 TYR 0.014 0.002 TYR H 41 PHE 0.014 0.002 PHE A 68 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.19 (25202) covalent geometry : angle 0.66577 / 0.44 (36484) hydrogen bonds : bond 0.07858 / 5.21 ( 1476) hydrogen bonds : angle 3.80387 / 2.78 ( 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 323 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.654 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: C 65 GLU cc_start: 0.9341 (tt0) cc_final: 0.8952 (tp30) REVERT: G 69 ASN cc_start: 0.9265 (m-40) cc_final: 0.8870 (m110) REVERT: M 82 VAL cc_start: 0.6476 (t) cc_final: 0.6240 (t) REVERT: R 62 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9021 (tp30) REVERT: R 69 ASN cc_start: 0.8798 (m-40) cc_final: 0.8585 (t0) outliers start: 29 outliers final: 27 residues processed: 311 average time/residue: 0.3788 time to fit residues: 169.8947 Evaluate side-chains 298 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 B residue 85 MET 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 83 LEU 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 H residue 81 LEU 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 N residue 65 GLU Chi-restraints excluded: chain O residue 97 THR 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 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 195 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 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 = 0.4601 r_free = 0.4601 target = 0.108087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.091981 restraints weight = 540972.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.094036 restraints weight = 353185.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.095458 restraints weight = 255959.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.096430 restraints weight = 200756.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.097185 restraints weight = 167909.694| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25202 Z= 0.200 Angle : 0.675 8.644 36484 Z= 0.436 Chirality : 0.044 0.171 4144 Planarity : 0.005 0.047 2636 Dihedral : 30.112 87.945 7918 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.42 % Allowed : 15.86 % Favored : 81.72 % 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: 0.66 (0.20), residues: 1472 helix: 1.03 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 130 TYR 0.027 0.002 TYR Q 73 PHE 0.020 0.002 PHE F 101 HIS 0.007 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.20 (25202) covalent geometry : angle 0.67486 / 0.44 (36484) hydrogen bonds : bond 0.08257 / 5.43 ( 1476) hydrogen bonds : angle 3.83887 / 2.80 ( 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 307 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.678 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: B 73 TYR cc_start: 0.8784 (m-80) cc_final: 0.8237 (t80) REVERT: C 65 GLU cc_start: 0.9360 (tt0) cc_final: 0.8972 (tp30) REVERT: D 60 MET cc_start: 0.8319 (tpp) cc_final: 0.7973 (tpt) REVERT: G 69 ASN cc_start: 0.9321 (m-40) cc_final: 0.8629 (m110) REVERT: G 92 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7970 (mm-30) REVERT: M 82 VAL cc_start: 0.6417 (t) cc_final: 0.6174 (t) outliers start: 30 outliers final: 25 residues processed: 295 average time/residue: 0.3704 time to fit residues: 156.3251 Evaluate side-chains 285 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 B residue 58 VAL 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 106 GLU 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 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 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 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: 4.9990 chunk 123 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 0.2980 chunk 145 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.090819 restraints weight = 542512.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.092839 restraints weight = 353014.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.094248 restraints weight = 255733.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.095176 restraints weight = 200562.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.095932 restraints weight = 169146.802| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25202 Z= 0.172 Angle : 0.643 6.866 36484 Z= 0.419 Chirality : 0.042 0.173 4144 Planarity : 0.005 0.049 2636 Dihedral : 30.361 89.654 7918 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.74 % Allowed : 16.99 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1472 helix: 1.22 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.09 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.025 0.002 TYR M 89 PHE 0.012 0.002 PHE D 66 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 (25202) covalent geometry : angle 0.64280 / 0.42 (36484) hydrogen bonds : bond 0.06800 / 4.46 ( 1476) hydrogen bonds : angle 3.72185 / 2.70 ( 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 309 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9280 (mmm) cc_final: 0.9066 (mmm) REVERT: C 65 GLU cc_start: 0.9377 (tt0) cc_final: 0.8966 (tp30) REVERT: D 60 MET cc_start: 0.8289 (tpp) cc_final: 0.7913 (tpt) REVERT: G 69 ASN cc_start: 0.9067 (m-40) cc_final: 0.8661 (m110) REVERT: G 92 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7912 (mm-30) REVERT: M 82 VAL cc_start: 0.6278 (t) cc_final: 0.6038 (t) REVERT: R 36 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6616 (ttt180) outliers start: 34 outliers final: 26 residues processed: 294 average time/residue: 0.3808 time to fit residues: 161.3730 Evaluate side-chains 285 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain B residue 65 ASN 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 C residue 115 VAL Chi-restraints excluded: chain D residue 74 ILE 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 88 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 63 ILE 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 R residue 36 ARG 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: 10.0000 chunk 7 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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** D 50 HIS ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4555 r_free = 0.4555 target = 0.104386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.088369 restraints weight = 549739.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.090356 restraints weight = 359697.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.091743 restraints weight = 261613.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.092630 restraints weight = 205493.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.093254 restraints weight = 173345.084| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25202 Z= 0.207 Angle : 0.658 6.984 36484 Z= 0.427 Chirality : 0.043 0.204 4144 Planarity : 0.005 0.036 2636 Dihedral : 30.442 89.550 7918 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.82 % Allowed : 18.04 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1472 helix: 1.03 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.021 0.002 TYR M 89 PHE 0.012 0.002 PHE A 68 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.21 (25202) covalent geometry : angle 0.65837 / 0.43 (36484) hydrogen bonds : bond 0.08646 / 5.66 ( 1476) hydrogen bonds : angle 3.96575 / 2.87 ( 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: 35 poor density : 257 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: 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: 0.9384 (tt0) cc_final: 0.9006 (tp30) REVERT: D 60 MET cc_start: 0.8296 (tpp) cc_final: 0.7970 (tpt) REVERT: G 51 TYR cc_start: 0.8917 (m-80) cc_final: 0.8339 (m-80) REVERT: G 69 ASN cc_start: 0.9033 (m-40) cc_final: 0.8715 (m110) REVERT: R 36 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6390 (tpp-160) outliers start: 35 outliers final: 30 residues processed: 277 average time/residue: 0.4026 time to fit residues: 159.7742 Evaluate side-chains 277 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain 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 106 GLU 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 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 74 THR 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 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 R residue 36 ARG Chi-restraints excluded: chain S residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 197 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 180 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 190 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.100064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.084340 restraints weight = 559487.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.086197 restraints weight = 365518.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.087472 restraints weight = 267276.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.088438 restraints weight = 211903.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.088975 restraints weight = 177598.854| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 25202 Z= 0.226 Angle : 0.702 11.079 36484 Z= 0.446 Chirality : 0.044 0.230 4144 Planarity : 0.005 0.042 2636 Dihedral : 30.775 87.682 7918 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.54 % Allowed : 17.71 % Favored : 78.74 % 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: 0.08 (0.20), residues: 1472 helix: 0.61 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 79 TYR 0.026 0.003 TYR M 89 PHE 0.015 0.002 PHE B 62 HIS 0.012 0.002 HIS S 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.23 (25202) covalent geometry : angle 0.70183 / 0.45 (36484) hydrogen bonds : bond 0.10306 / 6.75 ( 1476) hydrogen bonds : angle 4.26527 / 3.08 ( 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 287 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.884 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: C 65 GLU cc_start: 0.9384 (tt0) cc_final: 0.8998 (tp30) REVERT: D 60 MET cc_start: 0.8301 (tpp) cc_final: 0.7938 (tpt) REVERT: G 51 TYR cc_start: 0.8940 (m-80) cc_final: 0.8339 (m-80) REVERT: G 69 ASN cc_start: 0.9105 (m-40) cc_final: 0.8759 (m110) REVERT: L 105 PHE cc_start: 0.9661 (m-80) cc_final: 0.9338 (m-10) REVERT: M 54 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: R 36 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6424 (tpp-160) outliers start: 44 outliers final: 38 residues processed: 269 average time/residue: 0.3964 time to fit residues: 153.8439 Evaluate side-chains 270 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 109 ASN 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 74 THR 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 61 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 18 ARG 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 L residue 114 HIS Chi-restraints excluded: chain M residue 54 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 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 Q residue 38 LEU Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 65 GLU 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: 9.9990 chunk 166 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 192 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 174 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 49 optimal weight: 0.6980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.101477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.085708 restraints weight = 555052.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.087640 restraints weight = 359340.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.088914 restraints weight = 261160.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.089846 restraints weight = 207424.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.090402 restraints weight = 174176.516| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25202 Z= 0.166 Angle : 0.656 8.199 36484 Z= 0.419 Chirality : 0.042 0.203 4144 Planarity : 0.005 0.038 2636 Dihedral : 30.828 86.872 7918 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.58 % Allowed : 19.24 % Favored : 78.18 % 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: 0.78 (0.21), residues: 1472 helix: 1.20 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 43 TYR 0.016 0.002 TYR M 89 PHE 0.012 0.001 PHE H 66 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.17 (25202) covalent geometry : angle 0.65650 / 0.42 (36484) hydrogen bonds : bond 0.07333 / 4.80 ( 1476) hydrogen bonds : angle 3.91858 / 2.83 ( 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 273 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.645 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: C 65 GLU cc_start: 0.9388 (tt0) cc_final: 0.8963 (tp30) REVERT: C 92 GLU cc_start: 0.7741 (tp30) cc_final: 0.7541 (tp30) REVERT: E 91 MET cc_start: 0.7804 (mmp) cc_final: 0.7373 (mmp) REVERT: G 51 TYR cc_start: 0.8957 (m-80) cc_final: 0.8350 (m-80) REVERT: G 69 ASN cc_start: 0.9078 (m-40) cc_final: 0.8754 (m110) REVERT: L 105 PHE cc_start: 0.9649 (m-80) cc_final: 0.9280 (m-10) REVERT: M 54 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: M 85 MET cc_start: 0.6991 (tmm) cc_final: 0.6673 (ppp) REVERT: R 36 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6667 (ttt180) outliers start: 32 outliers final: 28 residues processed: 260 average time/residue: 0.4100 time to fit residues: 153.7176 Evaluate side-chains 264 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 44 VAL 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 106 GLU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG 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 54 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.100511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.084769 restraints weight = 558580.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.086675 restraints weight = 364192.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.087972 restraints weight = 265140.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.088945 restraints weight = 209722.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.089502 restraints weight = 175090.580| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25202 Z= 0.185 Angle : 0.657 7.327 36484 Z= 0.421 Chirality : 0.042 0.202 4144 Planarity : 0.005 0.040 2636 Dihedral : 30.826 86.403 7918 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.90 % Allowed : 19.40 % Favored : 77.70 % 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: 0.71 (0.20), residues: 1472 helix: 1.14 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.020 0.002 TYR Q 89 PHE 0.022 0.002 PHE S 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.18 (25202) covalent geometry : angle 0.65721 / 0.42 (36484) hydrogen bonds : bond 0.08006 / 5.22 ( 1476) hydrogen bonds : angle 3.98792 / 2.88 ( 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 271 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.895 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: C 65 GLU cc_start: 0.9372 (tt0) cc_final: 0.8985 (tp30) REVERT: C 92 GLU cc_start: 0.7769 (tp30) cc_final: 0.7560 (tp30) REVERT: G 51 TYR cc_start: 0.8949 (m-80) cc_final: 0.8343 (m-80) REVERT: G 69 ASN cc_start: 0.9071 (m-40) cc_final: 0.8807 (m110) REVERT: L 105 PHE cc_start: 0.9663 (m-80) cc_final: 0.9295 (m-10) REVERT: M 54 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: R 36 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6685 (ttt180) outliers start: 36 outliers final: 32 residues processed: 255 average time/residue: 0.4087 time to fit residues: 148.9663 Evaluate side-chains 263 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 44 VAL 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 86 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG 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 54 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 101 LEU 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 Q residue 38 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 170 optimal weight: 50.0000 chunk 176 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.095722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.080283 restraints weight = 576523.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.082086 restraints weight = 376020.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.083302 restraints weight = 274635.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.084183 restraints weight = 218090.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.084744 restraints weight = 183916.057| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.7495 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= 0.247 Angle : 0.733 9.398 36484 Z= 0.460 Chirality : 0.045 0.199 4144 Planarity : 0.006 0.099 2636 Dihedral : 31.099 89.631 7918 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.66 % Allowed : 19.73 % Favored : 77.62 % 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 (0.20), residues: 1472 helix: 0.35 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG S 100 TYR 0.019 0.002 TYR S 41 PHE 0.026 0.002 PHE P 79 HIS 0.009 0.002 HIS M 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.25 (25202) covalent geometry : angle 0.73296 / 0.46 (36484) hydrogen bonds : bond 0.12302 / 8.06 ( 1476) hydrogen bonds : angle 4.47838 / 3.24 ( 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 255 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.585 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: B 73 TYR cc_start: 0.8875 (m-80) cc_final: 0.8590 (m-80) REVERT: C 65 GLU cc_start: 0.9417 (tt0) cc_final: 0.8852 (tp30) REVERT: C 69 ASN cc_start: 0.8383 (m-40) cc_final: 0.7726 (m-40) REVERT: D 72 GLU cc_start: 0.8941 (tp30) cc_final: 0.8575 (tm-30) REVERT: E 91 MET cc_start: 0.7930 (mmp) cc_final: 0.7532 (mmp) REVERT: G 51 TYR cc_start: 0.9082 (m-80) cc_final: 0.8419 (m-80) REVERT: G 69 ASN cc_start: 0.9071 (m-40) cc_final: 0.8742 (m110) REVERT: L 105 PHE cc_start: 0.9712 (m-80) cc_final: 0.9365 (m-10) REVERT: M 54 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8518 (pt0) REVERT: R 36 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6452 (tpp-160) outliers start: 33 outliers final: 27 residues processed: 239 average time/residue: 0.3824 time to fit residues: 131.5840 Evaluate side-chains 246 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 93 LEU 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 18 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 95 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 54 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 95 ASN 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: 5.9990 chunk 169 optimal weight: 0.8980 chunk 192 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 187 optimal weight: 50.0000 chunk 60 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 0.1980 chunk 143 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.098300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.082742 restraints weight = 567614.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.084583 restraints weight = 366968.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.085923 restraints weight = 267072.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.086880 restraints weight = 209692.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.087402 restraints weight = 175324.306| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25202 Z= 0.163 Angle : 0.666 7.707 36484 Z= 0.423 Chirality : 0.042 0.207 4144 Planarity : 0.005 0.041 2636 Dihedral : 31.154 89.839 7918 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.09 % Allowed : 20.37 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1472 helix: 1.03 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 100 TYR 0.021 0.002 TYR Q 89 PHE 0.025 0.002 PHE P 79 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 (25202) covalent geometry : angle 0.66597 / 0.42 (36484) hydrogen bonds : bond 0.07482 / 4.89 ( 1476) hydrogen bonds : angle 3.99288 / 2.88 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9446.01 seconds wall clock time: 160 minutes 42.15 seconds (9642.15 seconds total)