Starting phenix.real_space_refine on Sat Jul 4 18:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.map" model { file = "/net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v96_31810/07_2026/7v96_31810.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 549 5.49 5 S 28 5.16 5 C 13350 2.51 5 N 4535 2.21 5 O 5506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23968 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5818 Classifications: {'DNA': 275} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 274} Chain: "J" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5454 Classifications: {'DNA': 275} Link IDs: {'rna3p': 274} Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 826 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "L" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "M" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Q" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Time building chain proxies: 4.59, per 1000 atoms: 0.19 Number of scatterers: 23968 At special positions: 0 Unit cell: (136.422, 141.57, 120.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 549 15.00 O 5506 8.00 N 4535 7.00 C 13350 6.00 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: 1.59 Conformation dependent library (CDL) restraints added in 643.5 milliseconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 13 sheets defined 58.9% alpha, 1.6% beta 188 base pairs and 478 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.906A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.842A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.524A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.757A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.300A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.554A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.822A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 82 removed outlier: 3.541A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 removed outlier: 3.858A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.927A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.761A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.518A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.764A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.921A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 3.987A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.719A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 46 through 61 removed outlier: 3.841A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 removed outlier: 3.817A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.675A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.540A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.522A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.986A pdb=" N PHE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.527A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.913A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.840A pdb=" N ARG K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.559A pdb=" N ARG K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.758A pdb=" N VAL K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN K 125 " --> pdb=" O PRO K 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 42 removed outlier: 4.160A pdb=" N ARG L 39 " --> pdb=" O ARG L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.809A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.646A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG L 92 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.753A pdb=" N ALA M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 36 removed outlier: 3.551A pdb=" N ARG M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 51 removed outlier: 3.806A pdb=" N TYR M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 66 removed outlier: 3.557A pdb=" N LEU M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.821A pdb=" N ASP M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.680A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN M 84 " --> pdb=" O PRO M 80 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 116 removed outlier: 3.546A pdb=" N LEU M 115 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.724A pdb=" N VAL N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 removed outlier: 4.221A pdb=" N PHE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN N 64 " --> pdb=" O ASN N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.993A pdb=" N VAL N 95 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 removed outlier: 3.938A pdb=" N SER N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR N 118 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 70 through 74 removed outlier: 3.581A pdb=" N ILE O 74 " --> pdb=" O VAL O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 4.388A pdb=" N GLU O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.860A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN O 125 " --> pdb=" O PRO O 121 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG O 129 " --> pdb=" O GLN O 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 Processing helix chain 'P' and resid 31 through 34 Processing helix chain 'P' and resid 35 through 40 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.876A pdb=" N ARG P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.755A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS P 91 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG P 92 " --> pdb=" O TYR P 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 28 through 37 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.326A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU Q 58 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 88 removed outlier: 3.553A pdb=" N LEU Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 95 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.820A pdb=" N VAL R 38 " --> pdb=" O TYR R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 68 through 82 removed outlier: 3.758A pdb=" N ALA R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.883A pdb=" N LYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS R 113 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.444A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.597A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.089A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.781A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.234A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.668A pdb=" N TYR L 98 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.431A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 84 removed outlier: 7.460A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'Q' and resid 77 through 78 506 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 451 hydrogen bonds 856 hydrogen bond angles 0 basepair planarities 188 basepair parallelities 478 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2681 1.31 - 1.43: 8755 1.43 - 1.56: 12926 1.56 - 1.68: 1097 1.68 - 1.81: 48 Bond restraints: 25507 Sorted by residual: bond pdb=" C1' DC J 161 " pdb=" N1 DC J 161 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.48e+01 bond pdb=" N MET O 120 " pdb=" CA MET O 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.25e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.24e+01 bond pdb=" CA SER H 35 " pdb=" CB SER H 35 " ideal model delta sigma weight residual 1.536 1.471 0.064 1.42e-02 4.96e+03 2.06e+01 bond pdb=" CA SER H 84 " pdb=" CB SER H 84 " ideal model delta sigma weight residual 1.536 1.465 0.071 1.58e-02 4.01e+03 2.02e+01 ... (remaining 25502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 35327 3.55 - 7.09: 1333 7.09 - 10.64: 89 10.64 - 14.19: 5 14.19 - 17.73: 3 Bond angle restraints: 36757 Sorted by residual: angle pdb=" N VAL O 89 " pdb=" CA VAL O 89 " pdb=" C VAL O 89 " ideal model delta sigma weight residual 112.90 104.09 8.81 9.60e-01 1.09e+00 8.42e+01 angle pdb=" N VAL A 89 " pdb=" CA VAL A 89 " pdb=" C VAL A 89 " ideal model delta sigma weight residual 112.17 103.71 8.46 9.50e-01 1.11e+00 7.93e+01 angle pdb=" N ARG B 55 " pdb=" CA ARG B 55 " pdb=" C ARG B 55 " ideal model delta sigma weight residual 113.50 103.47 10.03 1.23e+00 6.61e-01 6.65e+01 angle pdb=" CA MET K 120 " pdb=" C MET K 120 " pdb=" N PRO K 121 " ideal model delta sigma weight residual 117.68 123.30 -5.62 7.10e-01 1.98e+00 6.26e+01 angle pdb=" CA MET E 120 " pdb=" C MET E 120 " pdb=" N PRO E 121 " ideal model delta sigma weight residual 117.68 123.21 -5.53 7.10e-01 1.98e+00 6.06e+01 ... (remaining 36752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 10735 35.66 - 71.33: 3252 71.33 - 106.99: 74 106.99 - 142.66: 8 142.66 - 178.32: 8 Dihedral angle restraints: 14077 sinusoidal: 9466 harmonic: 4611 Sorted by residual: dihedral pdb=" C ARG E 128 " pdb=" N ARG E 128 " pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " ideal model delta harmonic sigma weight residual -122.60 -137.84 15.24 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" C HIS H 79 " pdb=" N HIS H 79 " pdb=" CA HIS H 79 " pdb=" CB HIS H 79 " ideal model delta harmonic sigma weight residual -122.60 -137.11 14.51 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C ASN L 64 " pdb=" N ASN L 64 " pdb=" CA ASN L 64 " pdb=" CB ASN L 64 " ideal model delta harmonic sigma weight residual -122.60 -136.89 14.29 0 2.50e+00 1.60e-01 3.27e+01 ... (remaining 14074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 4025 0.254 - 0.508: 127 0.508 - 0.762: 6 0.762 - 1.016: 0 1.016 - 1.269: 3 Chirality restraints: 4161 Sorted by residual: chirality pdb=" C3' DC J 213 " pdb=" C4' DC J 213 " pdb=" O3' DC J 213 " pdb=" C2' DC J 213 " both_signs ideal model delta sigma weight residual False -2.73 -1.46 -1.27 2.00e-01 2.50e+01 4.03e+01 chirality pdb=" C3' DT J 102 " pdb=" C4' DT J 102 " pdb=" O3' DT J 102 " pdb=" C2' DT J 102 " both_signs ideal model delta sigma weight residual False -2.73 -1.70 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C3' DA J 242 " pdb=" C4' DA J 242 " pdb=" O3' DA J 242 " pdb=" C2' DA J 242 " both_signs ideal model delta sigma weight residual False -2.73 -1.71 -1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 4158 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 10 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ALA Q 10 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA Q 10 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG Q 11 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 80 " 0.010 2.00e-02 2.50e+03 1.73e-02 8.18e+00 pdb=" N9 DA J 80 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DA J 80 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DA J 80 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 80 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA J 80 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA J 80 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DA J 80 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA J 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 242 " 0.036 2.00e-02 2.50e+03 1.70e-02 7.96e+00 pdb=" N9 DA J 242 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 242 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 242 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 242 " -0.008 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 25 2.49 - 3.09: 14461 3.09 - 3.70: 37263 3.70 - 4.30: 59383 4.30 - 4.90: 83199 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O4' DC J 173 " pdb=" OP1 DT J 174 " model vdw 1.891 3.040 nonbonded pdb=" OP1 DC J 173 " pdb=" O4' DC J 173 " model vdw 2.099 3.040 nonbonded pdb=" O ASN M 73 " pdb=" OD1 ASN M 73 " model vdw 2.113 3.040 nonbonded pdb=" C4 DC J 173 " pdb=" O4 DT J 174 " model vdw 2.295 3.260 nonbonded pdb=" C1' DC J 173 " pdb=" OP1 DT J 174 " model vdw 2.329 3.470 ... (remaining 194326 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' and resid 36 through 134) selection = (chain 'E' and resid 36 through 134) selection = chain 'K' selection = (chain 'O' and resid 36 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) selection = (chain 'L' and resid 19 through 102) selection = chain 'P' } ncs_group { reference = (chain 'C' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'M' and resid 11 through 118) selection = (chain 'Q' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) } ncs_group { reference = (chain 'D' and resid 24 through 121) selection = chain 'H' selection = (chain 'N' and resid 24 through 121) selection = chain 'R' } 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: 1.000 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.950 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.011 0.083 25507 Z= 0.767 Angle : 1.554 17.732 36757 Z= 1.135 Chirality : 0.112 1.269 4161 Planarity : 0.007 0.030 2744 Dihedral : 30.755 178.319 11103 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.74 % Favored : 94.49 % Rotamer: Outliers : 15.66 % Allowed : 16.04 % Favored : 68.30 % Cbeta Deviations : 2.35 % 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: -1.38 (0.20), residues: 1561 helix: -0.33 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -1.79 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 76 TYR 0.029 0.003 TYR N 34 PHE 0.022 0.003 PHE K 78 HIS 0.010 0.002 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.01079 / 0.77 (25507) covalent geometry : angle 1.55443 / 1.14 (36757) hydrogen bonds : bond 0.26051 / 28.72 ( 957) hydrogen bonds : angle 11.06712 / 14.30 ( 2305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 256 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 79 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: B 88 TYR cc_start: 0.8358 (m-10) cc_final: 0.8102 (m-10) REVERT: B 92 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: B 95 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7981 (ttp-110) REVERT: C 13 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6645 (tptt) REVERT: C 74 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7955 (mtpt) REVERT: D 30 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7328 (mtp-110) REVERT: D 54 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7364 (tptt) REVERT: D 56 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7750 (tpt) REVERT: E 42 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7446 (mtm-85) REVERT: E 50 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: E 70 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8619 (tt) REVERT: G 24 GLN cc_start: 0.7607 (mm110) cc_final: 0.7198 (mp10) REVERT: G 73 ASN cc_start: 0.8012 (m-40) cc_final: 0.7807 (t0) REVERT: G 78 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (mm) REVERT: G 94 ASN cc_start: 0.9311 (t0) cc_final: 0.8775 (t0) REVERT: G 99 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6615 (mmt180) REVERT: G 110 ASN cc_start: 0.8227 (t0) cc_final: 0.7302 (p0) REVERT: H 90 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: H 103 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8904 (mt) REVERT: K 36 LYS cc_start: -0.0587 (OUTLIER) cc_final: -0.2574 (mmtt) REVERT: L 44 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8202 (tttt) REVERT: L 95 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: M 13 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6149 (ptmm) REVERT: M 24 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7221 (mp10) REVERT: M 29 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8236 (mmm160) REVERT: M 34 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8734 (mp) REVERT: M 110 ASN cc_start: 0.8484 (t0) cc_final: 0.7441 (p0) REVERT: N 66 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mt) REVERT: N 76 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7801 (mtt90) REVERT: O 37 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.3972 (ttmt) REVERT: O 123 ASP cc_start: 0.9039 (m-30) cc_final: 0.8512 (m-30) REVERT: P 29 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8778 (mt) REVERT: P 53 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: P 88 TYR cc_start: 0.8519 (m-10) cc_final: 0.8112 (m-10) REVERT: P 92 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7954 (ttp80) REVERT: R 81 ASN cc_start: 0.8392 (m-40) cc_final: 0.8068 (m-40) outliers start: 208 outliers final: 58 residues processed: 416 average time/residue: 0.1995 time to fit residues: 118.3303 Evaluate side-chains 276 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 192 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 98 TYR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 43 PRO Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 102 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 64 ASN B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 104 GLN D 60 ASN D 81 ASN F 27 GLN F 75 HIS F 93 GLN G 84 GLN G 110 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 125 GLN M 84 GLN M 110 ASN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS R 81 ASN R 92 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142521 restraints weight = 34958.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141165 restraints weight = 79799.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142017 restraints weight = 77050.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143409 restraints weight = 48066.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143696 restraints weight = 39998.112| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25507 Z= 0.199 Angle : 0.808 10.396 36757 Z= 0.456 Chirality : 0.054 0.353 4161 Planarity : 0.005 0.035 2744 Dihedral : 33.261 178.107 8086 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.95 % Favored : 96.80 % Rotamer: Outliers : 7.23 % Allowed : 20.93 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1561 helix: -0.35 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.80 (0.22), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 63 TYR 0.027 0.002 TYR R 80 PHE 0.015 0.002 PHE D 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.20 (25507) covalent geometry : angle 0.80823 / 0.46 (36757) hydrogen bonds : bond 0.09379 / 10.84 ( 957) hydrogen bonds : angle 4.26841 / 5.83 ( 2305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 180 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: A 122 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8273 (mtmm) REVERT: B 27 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: B 75 HIS cc_start: 0.9141 (t70) cc_final: 0.8882 (t-90) REVERT: B 79 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8461 (mtmp) REVERT: B 92 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8070 (ttp80) REVERT: C 13 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6288 (tptt) REVERT: C 74 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8150 (mtpt) REVERT: D 30 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7224 (mtp-110) REVERT: E 42 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6523 (mtm-85) REVERT: E 122 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: G 78 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8135 (mt) REVERT: G 110 ASN cc_start: 0.8237 (t0) cc_final: 0.7043 (p0) REVERT: H 113 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6570 (ttpt) REVERT: H 117 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8484 (ttmt) REVERT: K 129 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7360 (ttm-80) REVERT: L 44 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8311 (ttmm) REVERT: M 13 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5372 (ptmt) REVERT: M 24 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7234 (mp10) REVERT: M 34 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8760 (mp) REVERT: N 56 MET cc_start: 0.8411 (mmp) cc_final: 0.8089 (tpt) REVERT: O 37 LYS cc_start: 0.5354 (OUTLIER) cc_final: 0.4202 (tttt) REVERT: O 122 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8274 (mtmm) REVERT: P 75 HIS cc_start: 0.8676 (t70) cc_final: 0.8324 (t70) REVERT: P 92 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7968 (ttp80) REVERT: R 49 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8505 (m) REVERT: R 86 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8515 (pt) REVERT: R 110 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7579 (tm-30) outliers start: 96 outliers final: 42 residues processed: 258 average time/residue: 0.1811 time to fit residues: 68.0737 Evaluate side-chains 213 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 122 LYS Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 156 optimal weight: 0.7980 chunk 204 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 81 ASN G 104 GLN K 68 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.184497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144559 restraints weight = 34907.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142509 restraints weight = 82278.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143333 restraints weight = 71919.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143582 restraints weight = 50355.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143914 restraints weight = 52760.622| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25507 Z= 0.149 Angle : 0.654 9.868 36757 Z= 0.388 Chirality : 0.046 0.340 4161 Planarity : 0.005 0.042 2744 Dihedral : 32.781 179.878 7980 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 5.42 % Allowed : 23.19 % Favored : 71.39 % 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: -1.14 (0.21), residues: 1561 helix: -0.20 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.65 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 20 TYR 0.028 0.002 TYR N 80 PHE 0.018 0.001 PHE D 67 HIS 0.007 0.001 HIS M 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (25507) covalent geometry : angle 0.65388 / 0.39 (36757) hydrogen bonds : bond 0.07632 / 8.79 ( 957) hydrogen bonds : angle 3.56128 / 4.80 ( 2305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: B 79 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8312 (mttp) REVERT: C 13 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6422 (tptt) REVERT: C 73 ASN cc_start: 0.7977 (m-40) cc_final: 0.7634 (t0) REVERT: C 74 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: D 30 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7285 (mtp-110) REVERT: D 80 TYR cc_start: 0.7926 (m-10) cc_final: 0.7691 (m-10) REVERT: E 129 ARG cc_start: 0.7141 (tmt170) cc_final: 0.6908 (tpt170) REVERT: H 113 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6814 (ttpt) REVERT: M 13 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5750 (ptmt) REVERT: M 34 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8911 (mp) REVERT: N 56 MET cc_start: 0.8391 (mmp) cc_final: 0.7949 (tpt) REVERT: N 66 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9012 (mm) REVERT: N 90 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: O 37 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4636 (tttt) REVERT: P 35 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.8027 (ttp-170) REVERT: P 53 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: Q 73 ASN cc_start: 0.7984 (m-40) cc_final: 0.7752 (t0) REVERT: R 56 MET cc_start: 0.7956 (tpp) cc_final: 0.7645 (tpp) REVERT: R 110 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: R 117 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7897 (ttmt) outliers start: 72 outliers final: 30 residues processed: 224 average time/residue: 0.1858 time to fit residues: 61.6123 Evaluate side-chains 179 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 40.0000 chunk 113 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 114 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 59 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN Q 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.181592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139032 restraints weight = 35021.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137176 restraints weight = 75241.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137900 restraints weight = 74649.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138183 restraints weight = 51442.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138456 restraints weight = 49740.718| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25507 Z= 0.155 Angle : 0.639 8.063 36757 Z= 0.376 Chirality : 0.045 0.328 4161 Planarity : 0.004 0.049 2744 Dihedral : 32.552 178.559 7939 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.07 % Favored : 96.73 % Rotamer: Outliers : 4.59 % Allowed : 24.17 % Favored : 71.23 % 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: -1.13 (0.21), residues: 1561 helix: -0.19 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.65 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.019 0.002 TYR L 88 PHE 0.012 0.001 PHE E 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (25507) covalent geometry : angle 0.63901 / 0.38 (36757) hydrogen bonds : bond 0.07114 / 8.19 ( 957) hydrogen bonds : angle 3.36853 / 4.49 ( 2305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.485 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: A 94 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7730 (tp30) REVERT: A 123 ASP cc_start: 0.8745 (m-30) cc_final: 0.8478 (m-30) REVERT: B 27 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: B 79 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8268 (mttp) REVERT: C 13 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6407 (tptt) REVERT: C 74 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7814 (mtpt) REVERT: C 112 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: D 30 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7334 (mtp-110) REVERT: D 80 TYR cc_start: 0.7913 (m-10) cc_final: 0.7533 (m-10) REVERT: H 110 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: H 113 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6903 (ttpt) REVERT: M 13 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5703 (ptmt) REVERT: N 56 MET cc_start: 0.8494 (mmp) cc_final: 0.8034 (tpt) REVERT: N 90 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: Q 84 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8209 (tp-100) REVERT: R 56 MET cc_start: 0.8054 (tpp) cc_final: 0.7682 (tpp) REVERT: R 80 TYR cc_start: 0.7963 (m-10) cc_final: 0.7208 (m-10) REVERT: R 110 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7521 (tm-30) outliers start: 61 outliers final: 36 residues processed: 200 average time/residue: 0.1800 time to fit residues: 54.1903 Evaluate side-chains 180 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 116 optimal weight: 0.0060 chunk 4 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 38 optimal weight: 50.0000 overall best weight: 3.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139478 restraints weight = 35130.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138507 restraints weight = 82068.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138938 restraints weight = 74714.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139356 restraints weight = 48496.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139418 restraints weight = 48944.156| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 25507 Z= 0.187 Angle : 0.644 7.814 36757 Z= 0.378 Chirality : 0.046 0.332 4161 Planarity : 0.005 0.039 2744 Dihedral : 32.446 176.573 7932 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 5.57 % Allowed : 24.55 % Favored : 69.88 % 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: -1.40 (0.21), residues: 1561 helix: -0.33 (0.17), residues: 1006 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 116 TYR 0.020 0.002 TYR N 34 PHE 0.013 0.002 PHE K 78 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (25507) covalent geometry : angle 0.64365 / 0.38 (36757) hydrogen bonds : bond 0.07546 / 8.73 ( 957) hydrogen bonds : angle 3.46918 / 4.63 ( 2305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 146 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: C 13 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6480 (tptt) REVERT: C 74 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7830 (mtpt) REVERT: C 112 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: D 30 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7360 (mtp-110) REVERT: F 92 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (mtp85) REVERT: H 59 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8929 (tpp) REVERT: H 113 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6872 (ttpp) REVERT: M 13 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5900 (ptmt) REVERT: N 56 MET cc_start: 0.8598 (mmp) cc_final: 0.8202 (tpt) REVERT: N 90 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: O 86 SER cc_start: 0.7620 (t) cc_final: 0.6755 (m) REVERT: P 92 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: R 56 MET cc_start: 0.8216 (tpp) cc_final: 0.7853 (tpp) REVERT: R 110 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7610 (tm-30) outliers start: 74 outliers final: 45 residues processed: 209 average time/residue: 0.1827 time to fit residues: 56.9327 Evaluate side-chains 195 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 135 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 chunk 103 optimal weight: 0.0570 chunk 25 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 80 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 84 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.181008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139332 restraints weight = 35203.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138740 restraints weight = 75567.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139252 restraints weight = 73315.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139036 restraints weight = 50943.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139384 restraints weight = 47951.691| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25507 Z= 0.138 Angle : 0.588 7.834 36757 Z= 0.352 Chirality : 0.043 0.309 4161 Planarity : 0.004 0.034 2744 Dihedral : 32.239 176.281 7924 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.41 % Rotamer: Outliers : 4.74 % Allowed : 25.23 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1561 helix: -0.15 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 76 TYR 0.016 0.001 TYR L 88 PHE 0.008 0.001 PHE D 67 HIS 0.003 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (25507) covalent geometry : angle 0.58827 / 0.35 (36757) hydrogen bonds : bond 0.06850 / 7.98 ( 957) hydrogen bonds : angle 3.19197 / 4.24 ( 2305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 138 time to evaluate : 0.623 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8743 (m-30) cc_final: 0.8429 (m-30) REVERT: B 27 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: C 13 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6513 (tptt) REVERT: C 74 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7761 (mtpt) REVERT: D 30 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7374 (mtp-110) REVERT: F 92 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8154 (mtp85) REVERT: G 34 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9190 (tt) REVERT: G 99 ARG cc_start: 0.7112 (tpt170) cc_final: 0.6841 (tpt170) REVERT: H 113 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6705 (ttpt) REVERT: M 13 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5888 (ptmt) REVERT: M 24 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7183 (mp10) REVERT: N 56 MET cc_start: 0.8474 (mmp) cc_final: 0.7913 (tpt) REVERT: N 76 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7646 (mtt180) REVERT: N 90 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: O 86 SER cc_start: 0.7545 (t) cc_final: 0.6739 (m) REVERT: R 110 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7528 (tm-30) outliers start: 63 outliers final: 39 residues processed: 190 average time/residue: 0.1729 time to fit residues: 48.8994 Evaluate side-chains 180 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 14 optimal weight: 40.0000 chunk 179 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 198 optimal weight: 0.1980 chunk 110 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 8 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 120 optimal weight: 0.6980 chunk 33 optimal weight: 40.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 110 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140331 restraints weight = 35071.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140044 restraints weight = 75767.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140453 restraints weight = 71359.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140215 restraints weight = 51213.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140544 restraints weight = 46068.406| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25507 Z= 0.130 Angle : 0.578 7.819 36757 Z= 0.346 Chirality : 0.042 0.311 4161 Planarity : 0.004 0.035 2744 Dihedral : 32.152 176.438 7924 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.90 % Rotamer: Outliers : 5.12 % Allowed : 25.53 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1561 helix: -0.02 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 23 TYR 0.031 0.001 TYR B 88 PHE 0.010 0.001 PHE K 78 HIS 0.007 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.13 (25507) covalent geometry : angle 0.57766 / 0.35 (36757) hydrogen bonds : bond 0.06845 / 8.03 ( 957) hydrogen bonds : angle 3.12665 / 4.11 ( 2305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 0.464 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: C 13 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6534 (tptt) REVERT: C 23 LEU cc_start: 0.8310 (mt) cc_final: 0.8099 (mp) REVERT: C 74 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7704 (mtpt) REVERT: C 112 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7037 (mt0) REVERT: D 30 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7212 (mtp-110) REVERT: F 92 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8132 (mtp85) REVERT: G 34 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9189 (tt) REVERT: G 99 ARG cc_start: 0.7058 (tpt170) cc_final: 0.6818 (tpt170) REVERT: H 113 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6777 (ttpt) REVERT: M 13 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5865 (ptmm) REVERT: N 56 MET cc_start: 0.8526 (mmp) cc_final: 0.7940 (tpt) REVERT: N 76 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7709 (mtt180) REVERT: N 90 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: O 86 SER cc_start: 0.7477 (t) cc_final: 0.6681 (m) REVERT: O 131 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7459 (mtp-110) outliers start: 68 outliers final: 38 residues processed: 198 average time/residue: 0.1768 time to fit residues: 52.1718 Evaluate side-chains 182 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 40.0000 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 73 ASN D 81 ASN G 104 GLN O 39 HIS Q 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.180825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139574 restraints weight = 34796.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139038 restraints weight = 77723.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139489 restraints weight = 66809.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140061 restraints weight = 44730.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140147 restraints weight = 44709.827| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25507 Z= 0.139 Angle : 0.586 7.085 36757 Z= 0.348 Chirality : 0.042 0.312 4161 Planarity : 0.004 0.032 2744 Dihedral : 32.078 176.697 7924 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 4.59 % Allowed : 26.28 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.21), residues: 1561 helix: 0.02 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.024 0.002 TYR D 80 PHE 0.009 0.001 PHE K 78 HIS 0.005 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (25507) covalent geometry : angle 0.58638 / 0.35 (36757) hydrogen bonds : bond 0.06955 / 8.16 ( 957) hydrogen bonds : angle 3.12044 / 4.13 ( 2305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 0.624 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7780 (mm-30) REVERT: B 27 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: C 13 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6541 (tptt) REVERT: C 74 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: C 112 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: D 30 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7207 (mtp-110) REVERT: D 56 MET cc_start: 0.7680 (tpp) cc_final: 0.7455 (tpp) REVERT: G 99 ARG cc_start: 0.7153 (tpt170) cc_final: 0.6895 (tpt170) REVERT: H 35 SER cc_start: 0.9087 (m) cc_final: 0.8720 (t) REVERT: H 113 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6793 (ttpt) REVERT: M 13 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5895 (ptmm) REVERT: N 56 MET cc_start: 0.8546 (mmp) cc_final: 0.7986 (tpt) REVERT: N 76 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7805 (mtt180) REVERT: N 90 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: O 86 SER cc_start: 0.7451 (t) cc_final: 0.6637 (m) REVERT: O 131 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7339 (mtp-110) REVERT: P 92 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8123 (ttp80) REVERT: R 110 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7532 (tm-30) outliers start: 61 outliers final: 39 residues processed: 195 average time/residue: 0.1715 time to fit residues: 50.0552 Evaluate side-chains 184 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 45 optimal weight: 50.0000 chunk 79 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 46 HIS G 104 GLN Q 84 GLN R 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136116 restraints weight = 35063.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134431 restraints weight = 84050.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135274 restraints weight = 74198.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136100 restraints weight = 51423.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136307 restraints weight = 51428.388| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25507 Z= 0.163 Angle : 0.619 7.202 36757 Z= 0.361 Chirality : 0.044 0.319 4161 Planarity : 0.004 0.046 2744 Dihedral : 32.029 177.315 7922 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 4.52 % Allowed : 26.28 % Favored : 69.20 % 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: -1.06 (0.21), residues: 1561 helix: -0.08 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.030 0.002 TYR H 80 PHE 0.012 0.002 PHE K 78 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (25507) covalent geometry : angle 0.61905 / 0.36 (36757) hydrogen bonds : bond 0.07449 / 8.68 ( 957) hydrogen bonds : angle 3.28513 / 4.37 ( 2305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 142 time to evaluate : 0.634 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 27 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: C 13 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6512 (tptt) REVERT: C 74 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: C 112 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7024 (mt0) REVERT: D 56 MET cc_start: 0.7894 (tpp) cc_final: 0.7666 (tpp) REVERT: F 92 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8002 (mtp85) REVERT: H 35 SER cc_start: 0.9165 (m) cc_final: 0.8705 (t) REVERT: H 113 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6810 (ttpt) REVERT: L 84 MET cc_start: 0.8181 (tpt) cc_final: 0.7955 (tpt) REVERT: M 13 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5823 (ptmm) REVERT: N 56 MET cc_start: 0.8579 (mmp) cc_final: 0.8069 (tpt) REVERT: N 76 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7821 (mtt180) REVERT: N 90 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: O 86 SER cc_start: 0.7531 (t) cc_final: 0.6799 (m) REVERT: O 131 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7267 (mtp-110) REVERT: P 92 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8170 (ttp80) REVERT: Q 84 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8123 (tp-100) REVERT: R 110 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7633 (tm-30) outliers start: 60 outliers final: 42 residues processed: 193 average time/residue: 0.1636 time to fit residues: 46.9185 Evaluate side-chains 193 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 193 optimal weight: 0.2980 chunk 194 optimal weight: 0.0980 chunk 199 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 46 HIS D 81 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142953 restraints weight = 35013.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141873 restraints weight = 91109.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142771 restraints weight = 71110.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142681 restraints weight = 52229.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143024 restraints weight = 52147.791| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25507 Z= 0.125 Angle : 0.573 9.503 36757 Z= 0.343 Chirality : 0.042 0.304 4161 Planarity : 0.004 0.037 2744 Dihedral : 31.908 177.475 7918 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.46 % Allowed : 27.48 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1561 helix: 0.07 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 35 TYR 0.027 0.001 TYR H 80 PHE 0.007 0.001 PHE D 67 HIS 0.035 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.12 (25507) covalent geometry : angle 0.57343 / 0.34 (36757) hydrogen bonds : bond 0.06886 / 8.07 ( 957) hydrogen bonds : angle 3.08557 / 4.05 ( 2305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.575 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7737 (mm-30) REVERT: B 27 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: C 13 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.6535 (tptt) REVERT: C 74 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7687 (mtpt) REVERT: C 112 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: D 56 MET cc_start: 0.7671 (tpp) cc_final: 0.7394 (tpp) REVERT: F 92 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7982 (mtp85) REVERT: G 99 ARG cc_start: 0.7252 (tpt170) cc_final: 0.7017 (tpt170) REVERT: H 35 SER cc_start: 0.9043 (m) cc_final: 0.8648 (t) REVERT: H 113 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6909 (ttpt) REVERT: M 13 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5941 (ptmm) REVERT: M 29 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7961 (mmm160) REVERT: N 56 MET cc_start: 0.8489 (mmp) cc_final: 0.7952 (tpt) REVERT: N 76 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7721 (mtt180) REVERT: N 90 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: O 86 SER cc_start: 0.7465 (t) cc_final: 0.6781 (m) REVERT: R 110 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7567 (tm-30) outliers start: 46 outliers final: 31 residues processed: 177 average time/residue: 0.1742 time to fit residues: 46.2356 Evaluate side-chains 174 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 chunk 152 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 73 optimal weight: 0.1980 chunk 119 optimal weight: 7.9990 chunk 115 optimal weight: 0.0050 chunk 30 optimal weight: 50.0000 chunk 160 optimal weight: 0.6980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 81 ASN G 104 GLN Q 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.181229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139275 restraints weight = 34850.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138255 restraints weight = 80600.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139009 restraints weight = 73154.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139171 restraints weight = 48824.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139498 restraints weight = 48827.138| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 25507 Z= 0.167 Angle : 0.758 59.200 36757 Z= 0.479 Chirality : 0.042 0.304 4161 Planarity : 0.005 0.152 2744 Dihedral : 31.908 177.481 7911 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.31 % Allowed : 27.56 % Favored : 69.13 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1561 helix: 0.07 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 35 TYR 0.024 0.001 TYR H 80 PHE 0.008 0.001 PHE D 67 HIS 0.193 0.004 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.17 (25507) covalent geometry : angle 0.75780 / 0.48 (36757) hydrogen bonds : bond 0.06887 / 8.07 ( 957) hydrogen bonds : angle 3.07371 / 4.05 ( 2305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.67 seconds wall clock time: 47 minutes 2.41 seconds (2822.41 seconds total)