Starting phenix.real_space_refine on Sun Feb 8 08:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmm_48394/02_2026/9mmm_48394.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 570 5.49 5 S 28 5.16 5 C 13060 2.51 5 N 4428 2.21 5 O 5526 1.98 5 H 18934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "N" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "R" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1471 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "X" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4519 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Chain: "Y" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4552 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 7.52, per 1000 atoms: 0.18 Number of scatterers: 42546 At special positions: 0 Unit cell: (123.97, 127.05, 148.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 570 15.00 O 5526 8.00 N 4428 7.00 C 13060 6.00 H 18934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 775.0 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: 7.08 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: 8.64 Time building geometry restraints manager: 4.90 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=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ARG F 24 " pdb=" CA ARG F 24 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N SER O 33 " pdb=" CA SER O 33 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ARG Q 24 " pdb=" CA ARG Q 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 44131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 70028 1.32 - 2.65: 9198 2.65 - 3.97: 715 3.97 - 5.30: 58 5.30 - 6.62: 5 Bond angle restraints: 80004 Sorted by residual: angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 109.70 104.23 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C4' DC X 21 " pdb=" O4' DC X 21 " pdb=" C1' DC X 21 " ideal model delta sigma weight residual 109.70 104.26 5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C4' DC I 66 " pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " ideal model delta sigma weight residual 109.70 104.35 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C4' DC X 66 " pdb=" O4' DC X 66 " pdb=" C1' DC X 66 " ideal model delta sigma weight residual 109.70 104.41 5.29 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C2' DC I 69 " pdb=" C1' DC I 69 " pdb=" N1 DC I 69 " ideal model delta sigma weight residual 113.50 118.56 -5.06 1.50e+00 4.44e-01 1.14e+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 - 0.048: 2901 0.048 - 0.096: 1017 0.096 - 0.143: 191 0.143 - 0.191: 27 0.191 - 0.239: 8 Chirality restraints: 4144 Sorted by residual: chirality pdb=" C1' DC X 66 " pdb=" O4' DC X 66 " pdb=" C2' DC X 66 " pdb=" N1 DC X 66 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C4' DC I 69 " pdb=" C5' DC I 69 " pdb=" O4' DC I 69 " pdb=" C3' DC I 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4141 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " 0.024 9.50e-02 1.11e+02 3.95e-02 3.37e+01 pdb=" NE ARG C 33 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG C 33 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG C 33 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 33 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 33 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG C 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 33 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 33 " -0.023 9.50e-02 1.11e+02 3.93e-02 3.36e+01 pdb=" NE ARG N 33 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG N 33 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG N 33 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG N 33 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG N 33 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG N 33 " 0.073 2.00e-02 2.50e+03 pdb="HH21 ARG N 33 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG N 33 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 87 " 0.409 9.50e-02 1.11e+02 1.39e-01 3.30e+01 pdb=" NE ARG H 87 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG H 87 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 87 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG H 87 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG H 87 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 87 " 0.019 2.00e-02 2.50e+03 pdb="HH21 ARG H 87 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 87 " 0.046 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1191 2.19 - 2.79: 69352 2.79 - 3.39: 99139 3.39 - 4.00: 140985 4.00 - 4.60: 223275 Nonbonded interactions: 533942 Sorted by model distance: nonbonded pdb=" OE1 GLU P 74 " pdb="HD21 ASN Q 26 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU E 74 " pdb="HD21 ASN F 26 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP P 107 " pdb="HH11 ARG P 132 " model vdw 1.602 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP D 69 " pdb=" HH TYR F 99 " model vdw 1.611 2.450 ... (remaining 533937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) selection = chain 'M' selection = (chain 'Q' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.160 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.500 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.140 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25202 Z= 0.251 Angle : 0.912 6.621 36484 Z= 0.590 Chirality : 0.049 0.239 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 covalent geometry : bond 0.00532 (25202) covalent geometry : angle 0.91225 (36484) hydrogen bonds : bond 0.13253 ( 1476) hydrogen bonds : angle 3.78032 ( 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 : 0.895 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4310 time to fit residues: 303.5175 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 : 0.912 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 10.0000 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: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 96 GLN F 65 ASN M 26 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.106663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.090958 restraints weight = 547600.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.093031 restraints weight = 356359.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.094404 restraints weight = 254311.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.095413 restraints weight = 199332.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.096201 restraints weight = 165154.189| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 25202 Z= 0.292 Angle : 0.754 8.985 36484 Z= 0.464 Chirality : 0.048 0.168 4144 Planarity : 0.006 0.077 2636 Dihedral : 29.663 89.907 7922 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.42 % Allowed : 13.61 % 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: 1.23 (0.20), residues: 1472 helix: 1.37 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -0.59 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 100 TYR 0.018 0.003 TYR H 41 PHE 0.016 0.002 PHE P 68 HIS 0.008 0.002 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00602 (25202) covalent geometry : angle 0.75439 (36484) hydrogen bonds : bond 0.11401 ( 1476) hydrogen bonds : angle 3.92034 ( 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 347 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 ASN cc_start: 0.9290 (m-40) cc_final: 0.8869 (m110) REVERT: M 82 VAL cc_start: 0.6416 (t) cc_final: 0.6176 (t) REVERT: P 79 PHE cc_start: 0.8026 (t80) cc_final: 0.7554 (t80) REVERT: P 131 ILE cc_start: 0.9130 (mt) cc_final: 0.8838 (mt) REVERT: Q 69 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8392 (p0) REVERT: R 58 TYR cc_start: 0.8801 (t80) cc_final: 0.8561 (t80) REVERT: R 69 ASN cc_start: 0.8810 (m-40) cc_final: 0.8566 (t0) outliers start: 30 outliers final: 22 residues processed: 335 average time/residue: 0.4236 time to fit residues: 199.1996 Evaluate side-chains 294 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain M residue 64 GLU 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 83 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 69 ASP 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: 10.0000 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN M 76 HIS O 48 GLN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.105690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.089868 restraints weight = 549232.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.091954 restraints weight = 357038.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.093350 restraints weight = 256153.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.094377 restraints weight = 199540.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.095041 restraints weight = 164870.021| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25202 Z= 0.204 Angle : 0.676 6.423 36484 Z= 0.420 Chirality : 0.041 0.150 4144 Planarity : 0.005 0.039 2636 Dihedral : 29.811 88.921 7918 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.58 % Allowed : 15.14 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1472 helix: 1.45 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.031 0.002 TYR H 84 PHE 0.009 0.001 PHE D 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00429 (25202) covalent geometry : angle 0.67607 (36484) hydrogen bonds : bond 0.06501 ( 1476) hydrogen bonds : angle 3.63164 ( 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 311 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.853 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: B 69 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: B 73 TYR cc_start: 0.8776 (m-80) cc_final: 0.7909 (m-80) REVERT: G 69 ASN cc_start: 0.9348 (m-40) cc_final: 0.9021 (m110) REVERT: L 91 MET cc_start: 0.9555 (mmm) cc_final: 0.9122 (ptp) REVERT: L 105 PHE cc_start: 0.9603 (m-80) cc_final: 0.9254 (m-10) outliers start: 32 outliers final: 23 residues processed: 301 average time/residue: 0.3924 time to fit residues: 168.3323 Evaluate side-chains 279 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 ASP 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 H residue 81 LEU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN H 68 ASN L 40 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN N 74 ASN O 68 ASN P 69 GLN R 111 ASN S 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.094351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.079103 restraints weight = 584589.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.080913 restraints weight = 378425.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.082149 restraints weight = 274232.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.083042 restraints weight = 216501.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.083571 restraints weight = 181591.241| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 25202 Z= 0.343 Angle : 0.782 8.273 36484 Z= 0.479 Chirality : 0.051 0.233 4144 Planarity : 0.006 0.072 2636 Dihedral : 30.476 89.405 7918 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.35 % Allowed : 15.86 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1472 helix: 0.51 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.13 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 100 TYR 0.028 0.003 TYR M 89 PHE 0.016 0.002 PHE H 66 HIS 0.007 0.002 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00715 (25202) covalent geometry : angle 0.78227 (36484) hydrogen bonds : bond 0.13530 ( 1476) hydrogen bonds : angle 4.57088 ( 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 302 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 248 time to evaluate : 0.925 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: B 60 LYS cc_start: 0.9526 (tptt) cc_final: 0.9325 (tppt) REVERT: D 43 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 114 GLU cc_start: 0.9400 (tp30) cc_final: 0.8812 (tt0) REVERT: E 91 MET cc_start: 0.8091 (mmp) cc_final: 0.7741 (mmp) REVERT: G 39 HIS cc_start: 0.7898 (m90) cc_final: 0.7509 (m90) REVERT: G 69 ASN cc_start: 0.9399 (m-40) cc_final: 0.9118 (m110) REVERT: Q 69 ASP cc_start: 0.9372 (p0) cc_final: 0.9103 (p0) REVERT: R 36 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6521 (tpp-160) REVERT: R 62 GLU cc_start: 0.9556 (tp30) cc_final: 0.9309 (tm-30) outliers start: 54 outliers final: 40 residues processed: 281 average time/residue: 0.3912 time to fit residues: 158.2606 Evaluate side-chains 271 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 SER 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 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 B residue 92 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 43 TYR 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 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 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 96 GLN Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 95 ASN Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 95 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.098835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.083441 restraints weight = 566415.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.085331 restraints weight = 366955.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.086610 restraints weight = 266386.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.087545 restraints weight = 210730.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.088235 restraints weight = 175946.698| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25202 Z= 0.192 Angle : 0.672 7.659 36484 Z= 0.416 Chirality : 0.041 0.159 4144 Planarity : 0.005 0.047 2636 Dihedral : 30.428 89.560 7918 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.74 % Allowed : 18.60 % Favored : 78.66 % 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: 0.94 (0.20), residues: 1472 helix: 1.25 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 68 TYR 0.015 0.002 TYR M 89 PHE 0.012 0.001 PHE O 66 HIS 0.005 0.001 HIS O 110 Details of bonding type rmsd covalent geometry : bond 0.00403 (25202) covalent geometry : angle 0.67183 (36484) hydrogen bonds : bond 0.06442 ( 1476) hydrogen bonds : angle 3.85720 ( 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 281 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.943 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: B 73 TYR cc_start: 0.8758 (m-80) cc_final: 0.8454 (m-80) REVERT: D 43 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7297 (t80) REVERT: D 72 GLU cc_start: 0.8868 (tp30) cc_final: 0.8635 (tm-30) REVERT: G 39 HIS cc_start: 0.7915 (m90) cc_final: 0.7510 (m90) REVERT: G 51 TYR cc_start: 0.8738 (m-80) cc_final: 0.8458 (m-80) REVERT: G 69 ASN cc_start: 0.9378 (m-40) cc_final: 0.8758 (m110) REVERT: L 91 MET cc_start: 0.9592 (mmm) cc_final: 0.9180 (ptp) REVERT: N 96 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8767 (mmmt) REVERT: Q 69 ASP cc_start: 0.9340 (p0) cc_final: 0.9108 (p0) REVERT: R 36 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6616 (tpp-160) REVERT: R 62 GLU cc_start: 0.9538 (tp30) cc_final: 0.9283 (tm-30) REVERT: R 65 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8847 (tp30) REVERT: S 63 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7027 (mmm) outliers start: 34 outliers final: 25 residues processed: 267 average time/residue: 0.4151 time to fit residues: 159.2607 Evaluate side-chains 264 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 43 TYR 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 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain L residue 101 LEU 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 O residue 45 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 ASN R 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.091432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.076432 restraints weight = 597298.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.078186 restraints weight = 387947.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.079357 restraints weight = 281559.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.080153 restraints weight = 223435.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.080787 restraints weight = 189616.542| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.8571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 25202 Z= 0.311 Angle : 0.741 9.670 36484 Z= 0.457 Chirality : 0.048 0.190 4144 Planarity : 0.006 0.052 2636 Dihedral : 30.755 112.728 7918 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.67 % Allowed : 17.23 % Favored : 78.10 % 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: 0.05 (0.20), residues: 1472 helix: 0.57 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 100 TYR 0.018 0.002 TYR H 41 PHE 0.016 0.002 PHE A 68 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00648 (25202) covalent geometry : angle 0.74137 (36484) hydrogen bonds : bond 0.12321 ( 1476) hydrogen bonds : angle 4.53545 ( 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 276 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.942 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: B 65 ASN cc_start: 0.9487 (OUTLIER) cc_final: 0.9235 (p0) REVERT: D 43 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7264 (t80) REVERT: G 39 HIS cc_start: 0.8022 (m90) cc_final: 0.7705 (m-70) REVERT: G 69 ASN cc_start: 0.9079 (m-40) cc_final: 0.8765 (m110) REVERT: H 110 HIS cc_start: 0.9357 (m90) cc_final: 0.8994 (m-70) REVERT: L 105 PHE cc_start: 0.9725 (m-80) cc_final: 0.9393 (m-10) REVERT: Q 69 ASP cc_start: 0.9347 (p0) cc_final: 0.9117 (p0) REVERT: R 36 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6505 (tpp-160) REVERT: S 63 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6831 (mmm) outliers start: 58 outliers final: 44 residues processed: 256 average time/residue: 0.4312 time to fit residues: 157.6657 Evaluate side-chains 260 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL 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 B residue 92 LYS 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 43 TYR Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 95 ASN Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 95 ILE 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: 6.9990 chunk 197 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.089918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.075208 restraints weight = 600169.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.076974 restraints weight = 386813.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.078131 restraints weight = 279356.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.078987 restraints weight = 221579.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.079554 restraints weight = 186437.702| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.9534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 25202 Z= 0.275 Angle : 0.745 8.390 36484 Z= 0.458 Chirality : 0.045 0.175 4144 Planarity : 0.006 0.043 2636 Dihedral : 31.267 130.657 7918 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.83 % Allowed : 17.95 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1472 helix: 0.41 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 73 TYR 0.019 0.002 TYR H 41 PHE 0.016 0.002 PHE A 68 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00569 (25202) covalent geometry : angle 0.74538 (36484) hydrogen bonds : bond 0.09179 ( 1476) hydrogen bonds : angle 4.59058 ( 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 275 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.900 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: B 65 ASN cc_start: 0.9511 (OUTLIER) cc_final: 0.9250 (p0) REVERT: D 43 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7328 (t80) REVERT: H 100 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8809 (mmm160) REVERT: H 110 HIS cc_start: 0.9339 (m90) cc_final: 0.9135 (m-70) REVERT: Q 69 ASP cc_start: 0.9277 (p0) cc_final: 0.9063 (p0) REVERT: R 65 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8820 (tp30) REVERT: S 63 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7010 (mmm) outliers start: 60 outliers final: 46 residues processed: 256 average time/residue: 0.3919 time to fit residues: 142.8153 Evaluate side-chains 259 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 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 62 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 98 LEU 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 46 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 96 GLN 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 59 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 HIS 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 S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 95 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS P 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.090514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.076140 restraints weight = 598515.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.077815 restraints weight = 388056.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.079095 restraints weight = 277520.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.079658 restraints weight = 207243.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.079830 restraints weight = 190960.208| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.9796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25202 Z= 0.234 Angle : 0.696 7.737 36484 Z= 0.429 Chirality : 0.043 0.164 4144 Planarity : 0.005 0.046 2636 Dihedral : 31.150 139.168 7918 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.78 % Allowed : 20.05 % Favored : 76.17 % 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: 0.30 (0.21), residues: 1472 helix: 0.79 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : -1.26 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 68 TYR 0.013 0.002 TYR H 41 PHE 0.028 0.002 PHE P 79 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00488 (25202) covalent geometry : angle 0.69642 (36484) hydrogen bonds : bond 0.08746 ( 1476) hydrogen bonds : angle 4.27234 ( 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 266 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.852 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: B 27 ILE cc_start: 0.9495 (mp) cc_final: 0.9259 (tt) REVERT: C 92 GLU cc_start: 0.7281 (tp30) cc_final: 0.6811 (tp30) REVERT: D 43 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7371 (t80) REVERT: G 51 TYR cc_start: 0.9074 (m-80) cc_final: 0.8582 (m-80) REVERT: H 110 HIS cc_start: 0.9455 (m90) cc_final: 0.9167 (m90) REVERT: S 63 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7162 (mmm) REVERT: S 85 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8241 (p0) outliers start: 47 outliers final: 40 residues processed: 249 average time/residue: 0.3954 time to fit residues: 141.2971 Evaluate side-chains 254 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 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 43 TYR Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 LEU 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 46 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 96 GLN 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 59 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 95 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.073372 restraints weight = 610753.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.075080 restraints weight = 391586.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.076206 restraints weight = 283730.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.077017 restraints weight = 226052.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.077614 restraints weight = 190972.470| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 1.0383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 25202 Z= 0.276 Angle : 0.724 7.353 36484 Z= 0.447 Chirality : 0.046 0.168 4144 Planarity : 0.005 0.049 2636 Dihedral : 31.306 142.974 7918 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.03 % Allowed : 20.21 % Favored : 75.76 % 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: -0.05 (0.21), residues: 1472 helix: 0.51 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.27 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 100 TYR 0.020 0.002 TYR A 100 PHE 0.037 0.002 PHE P 79 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00576 (25202) covalent geometry : angle 0.72439 (36484) hydrogen bonds : bond 0.10232 ( 1476) hydrogen bonds : angle 4.54731 ( 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 259 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7305 (t80) REVERT: H 100 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8772 (mmm160) REVERT: H 110 HIS cc_start: 0.9383 (m90) cc_final: 0.9159 (m-70) REVERT: Q 69 ASP cc_start: 0.9152 (p0) cc_final: 0.8711 (p0) REVERT: R 65 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8782 (tp30) REVERT: S 63 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7147 (mmm) REVERT: S 85 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8297 (p0) outliers start: 50 outliers final: 42 residues processed: 239 average time/residue: 0.4301 time to fit residues: 146.4620 Evaluate side-chains 252 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 85 MET 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 46 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 96 GLN 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 59 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN P 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.089950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.075499 restraints weight = 599450.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.077282 restraints weight = 380575.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.078428 restraints weight = 274019.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.079286 restraints weight = 217853.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.079878 restraints weight = 183088.419| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 1.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25202 Z= 0.216 Angle : 0.692 7.117 36484 Z= 0.425 Chirality : 0.042 0.160 4144 Planarity : 0.005 0.046 2636 Dihedral : 31.264 141.609 7918 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.46 % Allowed : 21.18 % Favored : 75.36 % 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: 0.42 (0.21), residues: 1472 helix: 0.90 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 36 TYR 0.025 0.002 TYR A 100 PHE 0.028 0.002 PHE P 79 HIS 0.008 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00451 (25202) covalent geometry : angle 0.69210 (36484) hydrogen bonds : bond 0.07542 ( 1476) hydrogen bonds : angle 4.20520 ( 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 259 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7384 (t80) REVERT: H 110 HIS cc_start: 0.9458 (m90) cc_final: 0.9159 (m90) REVERT: Q 69 ASP cc_start: 0.9139 (p0) cc_final: 0.8789 (p0) REVERT: R 65 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8765 (tp30) REVERT: S 63 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7151 (mmm) outliers start: 43 outliers final: 36 residues processed: 242 average time/residue: 0.4239 time to fit residues: 147.8896 Evaluate side-chains 251 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 43 TYR Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 LEU 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 46 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 77 GLN 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 59 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 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 = 0.4406 r_free = 0.4406 target = 0.089882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075391 restraints weight = 603194.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.077100 restraints weight = 383586.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.078345 restraints weight = 278941.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.079120 restraints weight = 220105.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.079720 restraints weight = 186560.137| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 1.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 25202 Z= 0.232 Angle : 0.792 59.199 36484 Z= 0.490 Chirality : 0.042 0.159 4144 Planarity : 0.005 0.045 2636 Dihedral : 31.263 141.603 7918 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.38 % Allowed : 21.10 % Favored : 75.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1472 helix: 0.92 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.25 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 36 TYR 0.018 0.002 TYR A 100 PHE 0.023 0.002 PHE P 79 HIS 0.007 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00477 (25202) covalent geometry : angle 0.79192 (36484) hydrogen bonds : bond 0.07545 ( 1476) hydrogen bonds : angle 4.20635 ( 3662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10310.55 seconds wall clock time: 175 minutes 36.02 seconds (10536.02 seconds total)