Starting phenix.real_space_refine on Sun Sep 13 10:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v96_31810/09_2026/7v96_31810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v96_31810/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v96_31810/09_2026/7v96_31810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v96_31810/09_2026/7v96_31810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v96_31810/09_2026/7v96_31810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v96_31810/09_2026/7v96_31810.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 4.77, per 1000 atoms: 0.20 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: 1.74 Conformation dependent library (CDL) restraints added in 544.1 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: 3.44 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: 4.46 Time building geometry restraints manager: 2.46 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=" O3' DT J 144 " pdb=" P DA J 145 " ideal model delta sigma weight residual 1.607 1.671 -0.064 1.20e-02 6.94e+03 2.89e+01 bond pdb=" O3' DA J 80 " pdb=" P DC J 81 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.20e-02 6.94e+03 2.57e+01 bond pdb=" O3' DC J 171 " pdb=" P DC J 172 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.20e-02 6.94e+03 2.33e+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 ... (remaining 25502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 35321 3.55 - 7.09: 1339 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: 1.720 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- 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= 0.776 Angle : 1.558 17.732 36757 Z= 1.138 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 / 0.78 (25507) covalent geometry : angle 1.55781 / 1.14 (36757) hydrogen bonds : bond 0.26051 / 28.85 ( 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 : 0.506 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: 0.7098 (mp10) REVERT: B 79 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8331 (mttp) REVERT: B 88 TYR cc_start: 0.8358 (m-10) cc_final: 0.8105 (m-10) REVERT: B 92 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7950 (ttp80) REVERT: B 95 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7984 (ttp-110) REVERT: C 13 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6644 (tptt) REVERT: C 74 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7958 (mtpt) REVERT: D 30 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7334 (mtp-110) REVERT: D 54 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7357 (tptt) REVERT: D 56 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7748 (tpt) REVERT: E 50 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: E 70 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8611 (tt) REVERT: G 24 GLN cc_start: 0.7607 (mm110) cc_final: 0.7201 (mp10) REVERT: G 73 ASN cc_start: 0.8012 (m-40) cc_final: 0.7810 (t0) REVERT: G 78 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8582 (mm) REVERT: G 94 ASN cc_start: 0.9311 (t0) cc_final: 0.8777 (t0) REVERT: G 99 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6613 (mmt180) REVERT: G 104 GLN cc_start: 0.7976 (tt0) cc_final: 0.7775 (tt0) REVERT: G 110 ASN cc_start: 0.8227 (t0) cc_final: 0.7299 (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: 0.8903 (mt) REVERT: K 36 LYS cc_start: -0.0587 (OUTLIER) cc_final: -0.2618 (mmtt) REVERT: L 44 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8212 (tttt) REVERT: L 95 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8203 (mtp85) REVERT: M 13 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6154 (ptmm) REVERT: M 24 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7218 (mp10) REVERT: M 29 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8237 (mmm160) REVERT: M 34 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8737 (mp) REVERT: M 110 ASN cc_start: 0.8484 (t0) cc_final: 0.7440 (p0) REVERT: N 66 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9098 (mt) REVERT: N 76 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: O 37 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.3959 (tttt) REVERT: O 123 ASP cc_start: 0.9039 (m-30) cc_final: 0.8508 (m-30) REVERT: P 29 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8779 (mt) REVERT: P 53 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: P 88 TYR cc_start: 0.8519 (m-10) cc_final: 0.8110 (m-10) REVERT: P 92 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: R 26 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.3921 (mmp-170) REVERT: R 81 ASN cc_start: 0.8392 (m-40) cc_final: 0.8069 (m-40) outliers start: 208 outliers final: 58 residues processed: 416 average time/residue: 0.2128 time to fit residues: 126.4040 Evaluate side-chains 280 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 195 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 40 ARG 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 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 26 ARG 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: 0.7980 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: 0.9380 ------------------------------------------------------------------------------- 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 D 60 ASN D 81 ASN F 27 GLN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.180945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142651 restraints weight = 34903.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140758 restraints weight = 71127.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141325 restraints weight = 76194.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143209 restraints weight = 48954.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143560 restraints weight = 36289.009| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25507 Z= 0.185 Angle : 0.803 10.887 36757 Z= 0.454 Chirality : 0.055 0.376 4161 Planarity : 0.005 0.035 2744 Dihedral : 33.215 177.124 8090 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.01 % Favored : 96.67 % Rotamer: Outliers : 7.08 % Allowed : 20.86 % Favored : 72.06 % 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: -1.33 (0.20), residues: 1561 helix: -0.33 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.77 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 63 TYR 0.028 0.002 TYR R 80 PHE 0.015 0.002 PHE K 78 HIS 0.006 0.001 HIS M 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.19 (25507) covalent geometry : angle 0.80317 / 0.45 (36757) hydrogen bonds : bond 0.09434 / 10.95 ( 957) hydrogen bonds : angle 4.24261 / 5.82 ( 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 272 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 178 time to evaluate : 0.459 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: 0.8582 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: B 75 HIS cc_start: 0.9135 (t70) cc_final: 0.8860 (t-90) REVERT: B 79 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8449 (mtmp) REVERT: B 92 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8079 (ttp80) REVERT: C 13 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6206 (tptt) REVERT: C 74 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: D 30 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7367 (mtp-110) REVERT: E 56 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8303 (mtpp) REVERT: G 78 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8199 (mm) REVERT: G 110 ASN cc_start: 0.8269 (t0) cc_final: 0.7105 (p0) REVERT: H 113 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6583 (ttpt) REVERT: H 117 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8500 (ttmt) REVERT: K 129 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7334 (ttm-80) REVERT: L 44 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8334 (ttmm) REVERT: M 13 LYS cc_start: 0.5723 (OUTLIER) cc_final: 0.5267 (ptmt) REVERT: M 24 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7233 (mp10) REVERT: M 34 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8744 (mp) REVERT: N 56 MET cc_start: 0.8366 (mmp) cc_final: 0.8070 (tpt) REVERT: P 92 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7988 (ttp80) REVERT: R 26 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.4207 (mmp-170) REVERT: R 49 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8505 (m) REVERT: R 86 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8511 (pt) REVERT: R 110 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7646 (tm-30) outliers start: 94 outliers final: 43 residues processed: 254 average time/residue: 0.1814 time to fit residues: 68.4381 Evaluate side-chains 205 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 112 ILE 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 40 ARG 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 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 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 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 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 65 LEU Chi-restraints excluded: chain O residue 86 SER 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 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 26 ARG 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: 1.9990 chunk 204 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 81 ASN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 68 GLN Q 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133493 restraints weight = 35133.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129909 restraints weight = 54927.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130006 restraints weight = 78702.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131214 restraints weight = 51950.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132767 restraints weight = 40234.858| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25507 Z= 0.234 Angle : 0.779 9.232 36757 Z= 0.442 Chirality : 0.052 0.384 4161 Planarity : 0.006 0.040 2744 Dihedral : 32.910 179.072 7979 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.36 % Favored : 95.32 % Rotamer: Outliers : 7.53 % Allowed : 21.76 % Favored : 70.71 % 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: -1.90 (0.20), residues: 1561 helix: -0.77 (0.17), residues: 1003 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.052 0.003 TYR L 88 PHE 0.017 0.002 PHE D 67 HIS 0.015 0.002 HIS M 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (25507) covalent geometry : angle 0.77918 / 0.44 (36757) hydrogen bonds : bond 0.09169 / 10.41 ( 957) hydrogen bonds : angle 4.10287 / 5.56 ( 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 258 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 158 time to evaluate : 0.681 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: A 94 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7684 (tp30) REVERT: A 122 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: B 27 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: B 79 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8408 (mtmp) REVERT: B 92 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8107 (ttp80) REVERT: C 13 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6214 (tptt) REVERT: C 73 ASN cc_start: 0.8102 (m-40) cc_final: 0.7666 (t0) REVERT: C 74 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: D 30 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7269 (mtp-110) REVERT: E 63 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7404 (mmm-85) REVERT: E 129 ARG cc_start: 0.7464 (tmt170) cc_final: 0.7222 (tpt170) REVERT: G 99 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6352 (mmt180) REVERT: H 35 SER cc_start: 0.9311 (m) cc_final: 0.8903 (t) REVERT: H 113 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6683 (ttpt) REVERT: K 37 LYS cc_start: 0.3153 (OUTLIER) cc_final: 0.2005 (mmtm) REVERT: K 129 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7436 (tpm170) REVERT: L 62 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8543 (tt) REVERT: M 13 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5337 (ptmt) REVERT: N 90 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: O 37 LYS cc_start: 0.5819 (OUTLIER) cc_final: 0.4612 (tttt) REVERT: O 87 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8139 (t) REVERT: O 122 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: P 82 THR cc_start: 0.9265 (p) cc_final: 0.9064 (t) REVERT: P 92 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8058 (ttp80) REVERT: Q 73 ASN cc_start: 0.8138 (m-40) cc_final: 0.7728 (t0) REVERT: R 66 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9113 (mm) REVERT: R 110 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: R 117 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7666 (mttt) outliers start: 100 outliers final: 56 residues processed: 242 average time/residue: 0.2091 time to fit residues: 74.9184 Evaluate side-chains 218 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 142 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG 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 A residue 122 LYS 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 27 VAL Chi-restraints excluded: chain C residue 34 LEU 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 115 VAL 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 E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 31 LYS 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 37 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 K residue 129 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 77 LYS 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 M residue 115 LEU Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 34 TYR Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 87 THR 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 87 SER Chi-restraints excluded: chain O residue 89 VAL 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 73 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain R residue 26 ARG 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 66 ILE 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: 1.9990 chunk 33 optimal weight: 40.0000 chunk 113 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 4 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 0.0050 chunk 2 optimal weight: 50.0000 chunk 59 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Q 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140198 restraints weight = 35119.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137264 restraints weight = 55295.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137895 restraints weight = 58175.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139870 restraints weight = 43499.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139832 restraints weight = 34793.066| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25507 Z= 0.142 Angle : 0.632 8.716 36757 Z= 0.375 Chirality : 0.045 0.338 4161 Planarity : 0.004 0.029 2744 Dihedral : 32.514 179.171 7960 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 5.05 % Allowed : 25.15 % Favored : 69.80 % 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: -1.48 (0.21), residues: 1561 helix: -0.44 (0.17), residues: 1003 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 55 TYR 0.026 0.002 TYR N 80 PHE 0.012 0.001 PHE D 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (25507) covalent geometry : angle 0.63176 / 0.37 (36757) hydrogen bonds : bond 0.07159 / 8.29 ( 957) hydrogen bonds : angle 3.44703 / 4.66 ( 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 217 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.681 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7639 (tp30) REVERT: B 27 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: B 79 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: C 13 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6327 (tptt) REVERT: C 73 ASN cc_start: 0.7755 (m-40) cc_final: 0.7543 (t0) REVERT: C 74 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: D 30 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7257 (mtp-110) REVERT: H 35 SER cc_start: 0.9171 (m) cc_final: 0.8712 (t) REVERT: H 90 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8280 (mm-30) REVERT: H 113 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6912 (ttpt) REVERT: K 37 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.2099 (mmtm) REVERT: K 129 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7161 (ttm170) REVERT: L 77 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8765 (ttpp) REVERT: L 85 ASP cc_start: 0.8191 (m-30) cc_final: 0.7989 (m-30) REVERT: M 13 LYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5481 (ptmt) REVERT: M 24 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7312 (mp10) REVERT: N 76 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7740 (mtt180) REVERT: N 90 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: R 26 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.3847 (mmm160) REVERT: R 110 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: R 117 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7893 (ttmt) outliers start: 67 outliers final: 36 residues processed: 204 average time/residue: 0.1983 time to fit residues: 61.0995 Evaluate side-chains 189 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE 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 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 33 SER Chi-restraints excluded: chain D residue 51 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 G residue 34 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR 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 37 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 K residue 129 ARG 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 54 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 36 VAL 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 86 ILE Chi-restraints excluded: chain N residue 90 GLU 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 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 110 ASN Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 49 THR 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: 20.0000 chunk 41 optimal weight: 30.0000 chunk 37 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 116 optimal weight: 0.7980 chunk 4 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 38 optimal weight: 50.0000 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 104 GLN Q 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134126 restraints weight = 35137.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132754 restraints weight = 90293.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133397 restraints weight = 82784.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133590 restraints weight = 53340.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133872 restraints weight = 53718.360| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 25507 Z= 0.250 Angle : 0.749 8.544 36757 Z= 0.423 Chirality : 0.050 0.375 4161 Planarity : 0.005 0.039 2744 Dihedral : 32.488 177.353 7941 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.38 % Favored : 94.30 % Rotamer: Outliers : 6.93 % Allowed : 24.25 % Favored : 68.83 % 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: -2.03 (0.20), residues: 1561 helix: -0.80 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 129 TYR 0.024 0.002 TYR N 34 PHE 0.020 0.002 PHE K 78 HIS 0.006 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (25507) covalent geometry : angle 0.74874 / 0.42 (36757) hydrogen bonds : bond 0.08558 / 9.83 ( 957) hydrogen bonds : angle 3.82146 / 5.16 ( 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 230 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 138 time to evaluate : 0.688 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: A 94 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7626 (tm-30) REVERT: B 27 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: B 79 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: B 92 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8157 (ttp80) REVERT: C 13 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6522 (tptt) REVERT: C 73 ASN cc_start: 0.7780 (m-40) cc_final: 0.7482 (t0) REVERT: C 74 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7906 (mtpt) REVERT: C 112 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: D 30 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7384 (mtp-110) REVERT: D 56 MET cc_start: 0.8134 (tpp) cc_final: 0.7928 (tpp) REVERT: F 92 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8193 (mtp85) REVERT: G 99 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6298 (mmt180) REVERT: H 35 SER cc_start: 0.9269 (m) cc_final: 0.8816 (t) REVERT: H 113 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6833 (ttpt) REVERT: K 37 LYS cc_start: 0.3179 (OUTLIER) cc_final: 0.1942 (mmtm) REVERT: K 129 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7355 (tpm170) REVERT: M 13 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5767 (ptmt) REVERT: N 90 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: P 82 THR cc_start: 0.9242 (p) cc_final: 0.8981 (t) REVERT: P 92 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8167 (ttp80) REVERT: R 56 MET cc_start: 0.8337 (tpp) cc_final: 0.8101 (tpp) REVERT: R 110 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7735 (tm-30) outliers start: 92 outliers final: 56 residues processed: 215 average time/residue: 0.1997 time to fit residues: 64.3556 Evaluate side-chains 205 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 133 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 22 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR 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 86 VAL Chi-restraints excluded: chain B residue 92 ARG 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 33 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 49 ARG 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 E residue 130 ILE 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 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 39 TYR 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 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 37 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 K residue 129 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 77 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 54 VAL Chi-restraints excluded: chain N residue 36 VAL 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 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 26 ARG 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 Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 135 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 158 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 40.0000 chunk 80 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.179173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136319 restraints weight = 35108.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134588 restraints weight = 78373.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135475 restraints weight = 69510.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135728 restraints weight = 48984.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136098 restraints weight = 50560.963| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25507 Z= 0.135 Angle : 0.614 9.394 36757 Z= 0.365 Chirality : 0.044 0.335 4161 Planarity : 0.004 0.044 2744 Dihedral : 32.230 177.926 7937 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 4.44 % Allowed : 25.75 % Favored : 69.80 % 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: -1.60 (0.21), residues: 1561 helix: -0.52 (0.17), residues: 1019 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 88 TYR 0.018 0.001 TYR D 37 PHE 0.010 0.001 PHE D 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.14 (25507) covalent geometry : angle 0.61442 / 0.37 (36757) hydrogen bonds : bond 0.07122 / 8.31 ( 957) hydrogen bonds : angle 3.29596 / 4.40 ( 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: 59 poor density : 142 time to evaluate : 0.654 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: C 13 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6510 (tptt) REVERT: C 74 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7807 (mtpt) REVERT: C 112 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: D 30 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7339 (mtp-110) REVERT: E 63 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7319 (mmm-85) REVERT: F 92 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: H 35 SER cc_start: 0.9022 (m) cc_final: 0.8638 (t) REVERT: H 59 MET cc_start: 0.8906 (tpp) cc_final: 0.8607 (tpp) REVERT: H 90 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8079 (mm-30) REVERT: H 113 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6792 (ttpt) REVERT: K 37 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.2124 (tppt) REVERT: K 129 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7060 (ttm170) REVERT: M 13 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5770 (ptmt) REVERT: M 24 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7193 (mp10) REVERT: M 29 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7907 (mmm160) REVERT: O 86 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.6823 (m) REVERT: R 110 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7562 (tm-30) outliers start: 59 outliers final: 35 residues processed: 190 average time/residue: 0.1995 time to fit residues: 57.1905 Evaluate side-chains 184 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE 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 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 37 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 K residue 129 ARG 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 91 ILE 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 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 26 ARG 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: 30.0000 chunk 179 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 198 optimal weight: 0.0870 chunk 110 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 33 optimal weight: 40.0000 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS G 104 GLN H 81 ASN R 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138067 restraints weight = 35111.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136802 restraints weight = 84709.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137390 restraints weight = 80420.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137921 restraints weight = 53129.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138052 restraints weight = 52660.814| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25507 Z= 0.149 Angle : 0.615 7.973 36757 Z= 0.363 Chirality : 0.044 0.340 4161 Planarity : 0.004 0.032 2744 Dihedral : 32.189 177.843 7932 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 4.52 % Allowed : 26.13 % 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: -1.46 (0.21), residues: 1561 helix: -0.39 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.023 0.002 TYR B 88 PHE 0.010 0.001 PHE E 78 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (25507) covalent geometry : angle 0.61524 / 0.36 (36757) hydrogen bonds : bond 0.07276 / 8.48 ( 957) hydrogen bonds : angle 3.29984 / 4.40 ( 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 199 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.684 Fit side-chains 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: 0.8673 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: C 13 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6494 (tptt) REVERT: C 74 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7832 (mtpt) REVERT: C 112 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: D 30 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7399 (mtp-110) REVERT: F 92 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (mtp85) REVERT: H 35 SER cc_start: 0.8974 (m) cc_final: 0.8552 (t) REVERT: H 90 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7977 (mm-30) REVERT: H 113 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6843 (ttpt) REVERT: K 37 LYS cc_start: 0.3267 (OUTLIER) cc_final: 0.2098 (tppt) REVERT: K 129 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7050 (ttm170) REVERT: M 13 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5859 (ptmt) REVERT: M 24 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7209 (mp10) REVERT: M 29 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7898 (mmm160) REVERT: O 86 SER cc_start: 0.7556 (t) cc_final: 0.6786 (m) REVERT: P 35 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.8248 (ttp-170) REVERT: R 110 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7602 (tm-30) outliers start: 60 outliers final: 40 residues processed: 190 average time/residue: 0.2021 time to fit residues: 57.3552 Evaluate side-chains 185 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 49 ARG 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 22 LEU 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 D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 46 HIS 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 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 37 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 K residue 129 ARG 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 N residue 31 LYS Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 63 VAL 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 30 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 26 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 40.0000 chunk 91 optimal weight: 0.1980 chunk 32 optimal weight: 50.0000 chunk 110 optimal weight: 0.0470 chunk 22 optimal weight: 40.0000 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 50.0000 chunk 93 optimal weight: 0.0040 chunk 73 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 46 HIS 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 = 0.4151 r_free = 0.4151 target = 0.180846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142273 restraints weight = 34795.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140789 restraints weight = 86441.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141460 restraints weight = 78734.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141424 restraints weight = 51867.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141726 restraints weight = 53125.272| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25507 Z= 0.125 Angle : 0.582 8.154 36757 Z= 0.348 Chirality : 0.042 0.337 4161 Planarity : 0.004 0.035 2744 Dihedral : 32.040 178.226 7928 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 4.22 % Allowed : 27.11 % Favored : 68.67 % 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: -0.15 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.013 0.001 TYR R 37 PHE 0.008 0.001 PHE D 67 HIS 0.046 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.13 (25507) covalent geometry : angle 0.58178 / 0.35 (36757) hydrogen bonds : bond 0.06755 / 7.95 ( 957) hydrogen bonds : angle 3.08378 / 4.08 ( 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 199 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.659 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: C 13 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6548 (tptt) REVERT: C 74 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7689 (mtpt) REVERT: C 112 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: D 30 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7211 (mtp-110) REVERT: E 63 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7247 (mmm-85) REVERT: G 99 ARG cc_start: 0.7123 (tpt170) cc_final: 0.6872 (tpt170) REVERT: H 35 SER cc_start: 0.8909 (m) cc_final: 0.8572 (t) REVERT: H 90 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7999 (mm-30) REVERT: H 113 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6862 (ttpt) REVERT: K 37 LYS cc_start: 0.3269 (OUTLIER) cc_final: 0.2137 (tppt) REVERT: K 129 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7073 (ttm170) REVERT: M 13 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.5899 (ptmt) REVERT: M 24 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7208 (mp10) REVERT: M 29 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7953 (mmm160) REVERT: O 86 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.6754 (m) REVERT: P 35 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.8238 (ttp-170) REVERT: R 26 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.3932 (mmm160) REVERT: R 56 MET cc_start: 0.8157 (tpp) cc_final: 0.7913 (tpp) REVERT: R 110 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7493 (tm-30) outliers start: 56 outliers final: 34 residues processed: 189 average time/residue: 0.2100 time to fit residues: 58.6938 Evaluate side-chains 181 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 49 ARG 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 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL 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 37 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 K residue 129 ARG 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 N residue 31 LYS Chi-restraints excluded: chain N residue 39 TYR 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 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain R residue 26 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 chunk 173 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN D 81 ASN F 25 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139533 restraints weight = 34947.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138957 restraints weight = 75742.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139484 restraints weight = 70478.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139990 restraints weight = 46611.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140085 restraints weight = 46864.532| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25507 Z= 0.129 Angle : 0.583 7.974 36757 Z= 0.345 Chirality : 0.042 0.335 4161 Planarity : 0.004 0.032 2744 Dihedral : 31.954 178.347 7928 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 3.77 % Allowed : 27.71 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1561 helix: -0.02 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 116 TYR 0.012 0.001 TYR B 88 PHE 0.009 0.001 PHE E 104 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (25507) covalent geometry : angle 0.58321 / 0.35 (36757) hydrogen bonds : bond 0.06781 / 7.98 ( 957) hydrogen bonds : angle 3.04560 / 4.00 ( 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 191 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.694 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 SER cc_start: 0.7841 (t) cc_final: 0.6933 (m) REVERT: B 27 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: C 13 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6502 (tptt) REVERT: C 74 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7603 (mtpt) REVERT: C 112 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: D 30 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7237 (mtp-110) REVERT: D 56 MET cc_start: 0.7816 (tpp) cc_final: 0.7563 (tpp) REVERT: E 63 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7295 (mmm-85) REVERT: F 59 LYS cc_start: 0.8257 (tppt) cc_final: 0.6463 (tttt) REVERT: G 99 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6836 (tpt170) REVERT: H 35 SER cc_start: 0.8938 (m) cc_final: 0.8566 (t) REVERT: H 44 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6977 (tt0) REVERT: H 90 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7972 (mm-30) REVERT: H 113 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6852 (ttpt) REVERT: K 37 LYS cc_start: 0.3272 (OUTLIER) cc_final: 0.2098 (tppt) REVERT: K 129 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7105 (ttm170) REVERT: M 13 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5847 (ptmm) REVERT: M 29 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8063 (mmm160) REVERT: O 86 SER cc_start: 0.7512 (t) cc_final: 0.6863 (m) REVERT: P 35 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8264 (ttp-170) REVERT: R 26 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.3906 (mmm160) REVERT: R 110 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7531 (tm-30) outliers start: 50 outliers final: 32 residues processed: 182 average time/residue: 0.2037 time to fit residues: 55.6439 Evaluate side-chains 180 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 49 ARG 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 30 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 81 ASN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL 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 37 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 K residue 129 ARG 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 N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE 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 R residue 26 ARG 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: 0.6980 chunk 194 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 104 GLN Q 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139581 restraints weight = 34988.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137428 restraints weight = 60955.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137957 restraints weight = 70864.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139881 restraints weight = 46448.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140032 restraints weight = 34709.674| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 25507 Z= 0.159 Angle : 0.703 59.199 36757 Z= 0.427 Chirality : 0.042 0.333 4161 Planarity : 0.004 0.033 2744 Dihedral : 31.953 178.334 7928 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 3.54 % Allowed : 27.64 % Favored : 68.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1561 helix: -0.01 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.019 0.002 TYR N 37 PHE 0.009 0.001 PHE E 104 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (25507) covalent geometry : angle 0.70274 / 0.43 (36757) hydrogen bonds : bond 0.06766 / 7.96 ( 957) hydrogen bonds : angle 3.04501 / 4.01 ( 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 185 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.661 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 SER cc_start: 0.7859 (t) cc_final: 0.6968 (m) REVERT: B 27 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: C 13 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6444 (tptt) REVERT: C 74 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7595 (mtpt) REVERT: C 112 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7118 (mt0) REVERT: D 30 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7245 (mtp-110) REVERT: D 56 MET cc_start: 0.7799 (tpp) cc_final: 0.7515 (tpp) REVERT: E 63 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: F 59 LYS cc_start: 0.8219 (tppt) cc_final: 0.6475 (tttt) REVERT: G 99 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6837 (tpt170) REVERT: H 35 SER cc_start: 0.8880 (m) cc_final: 0.8610 (t) REVERT: H 44 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6980 (tt0) REVERT: H 90 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7974 (mm-30) REVERT: H 113 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6834 (ttpt) REVERT: K 37 LYS cc_start: 0.3393 (OUTLIER) cc_final: 0.2173 (tppt) REVERT: K 129 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7101 (ttm170) REVERT: M 13 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5722 (ptmm) REVERT: M 29 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8065 (mmm160) REVERT: O 86 SER cc_start: 0.7503 (t) cc_final: 0.6800 (m) REVERT: P 35 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8318 (ttp-170) REVERT: Q 84 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8060 (tp-100) REVERT: R 26 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.3829 (mmm160) REVERT: R 110 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7498 (tm-30) outliers start: 47 outliers final: 32 residues processed: 177 average time/residue: 0.2039 time to fit residues: 53.9251 Evaluate side-chains 181 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 49 ARG 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 30 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 E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL 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 37 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 K residue 129 ARG 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 N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE 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 Q residue 34 LEU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 26 ARG 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: 0.8980 chunk 180 optimal weight: 4.9990 chunk 32 optimal weight: 50.0000 chunk 73 optimal weight: 0.0070 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 160 optimal weight: 1.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.179926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139240 restraints weight = 34834.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137177 restraints weight = 65300.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137828 restraints weight = 73644.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139589 restraints weight = 46467.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139725 restraints weight = 37586.108| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25507 Z= 0.155 Angle : 0.704 57.042 36757 Z= 0.418 Chirality : 0.043 0.340 4161 Planarity : 0.004 0.034 2744 Dihedral : 31.948 178.367 7928 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 27.64 % Favored : 68.83 % 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: -1.01 (0.21), residues: 1561 helix: -0.05 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.041 0.002 TYR H 80 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (25507) covalent geometry : angle 0.70430 / 0.42 (36757) hydrogen bonds : bond 0.06850 / 8.05 ( 957) hydrogen bonds : angle 3.10228 / 4.05 ( 2305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.92 seconds wall clock time: 54 minutes 24.46 seconds (3264.46 seconds total)