Starting phenix.real_space_refine on Sun Dec 29 21:04:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyq_28692/12_2024/8eyq_28692.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14664 atoms to isotropic. 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 1525 5.49 5 S 54 5.16 5 C 24261 2.51 5 N 8995 2.21 5 O 13355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48190 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 32722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1525, 32722 Classifications: {'RNA': 1525} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 93, 'rna3p': 1, 'rna3p_pur': 745, 'rna3p_pyr': 563} Link IDs: {'rna2p': 215, 'rna3p': 1309} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 651 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Time building chain proxies: 18.96, per 1000 atoms: 0.39 Number of scatterers: 48190 At special positions: 0 Unit cell: (212.04, 172.71, 224.865, 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 54 16.00 P 1525 15.00 O 13355 8.00 N 8995 7.00 C 24261 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: 8.39 Conformation dependent library (CDL) restraints added in 2.0 seconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 41.4% alpha, 20.7% beta 486 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 16.81 Creating SS restraints... Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.652A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.832A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.591A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.569A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.701A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.872A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.685A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.704A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.528A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.615A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 46 through 51 removed outlier: 3.927A pdb=" N SER K 50 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 58 removed outlier: 3.501A pdb=" N ARG K 56 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 72 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.758A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ARG K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.518A pdb=" N LEU L 24 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 15 removed outlier: 3.581A pdb=" N PHE O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 41 removed outlier: 3.915A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 44 No H-bonds generated for 'chain 'O' and resid 42 through 44' Processing helix chain 'O' and resid 49 through 71 removed outlier: 3.705A pdb=" N ARG O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.856A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR O 79 " --> pdb=" O VAL O 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.735A pdb=" N VAL P 61 " --> pdb=" O ILE P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.692A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.711A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 33 removed outlier: 4.175A pdb=" N LYS R 30 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE R 33 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.765A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 64 removed outlier: 3.670A pdb=" N ALA R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 42 removed outlier: 3.642A pdb=" N GLN T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA T 17 " --> pdb=" O GLN T 13 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG T 18 " --> pdb=" O SER T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.601A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.942A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.555A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.680A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.715A pdb=" N ARG C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 144 removed outlier: 4.098A pdb=" N ALA C 133 " --> pdb=" O MET C 129 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 44 through 49 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.696A pdb=" N ASP I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 32 removed outlier: 4.763A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 removed outlier: 3.978A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.604A pdb=" N ALA M 18 " --> pdb=" O HIS M 14 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 61 removed outlier: 3.911A pdb=" N ILE M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 4.100A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 4.107A pdb=" N LEU M 89 " --> pdb=" O CYS M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.527A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 34 removed outlier: 4.148A pdb=" N LEU N 27 " --> pdb=" O LYS N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 48 removed outlier: 4.408A pdb=" N ASN N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.969A pdb=" N SER N 56 " --> pdb=" O ARG N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 91 Processing helix chain 'S' and resid 12 through 25 removed outlier: 3.815A pdb=" N LYS S 17 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 70 through 74 removed outlier: 3.997A pdb=" N GLU S 73 " --> pdb=" O LYS S 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.440A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.660A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 38 through 44 removed outlier: 3.610A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 44 removed outlier: 3.610A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.628A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'H' and resid 74 through 77 removed outlier: 5.719A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 41 through 45 removed outlier: 3.694A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU K 82 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE K 110 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL K 84 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP K 112 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL K 86 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 29 through 36 removed outlier: 6.875A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 8 through 11 removed outlier: 4.177A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 8 through 11 Processing sheet with id=AB5, first strand: chain 'Q' and resid 10 through 14 removed outlier: 6.773A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'C' and resid 52 through 58 removed outlier: 3.687A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.587A pdb=" N GLU C 166 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.587A pdb=" N GLU C 166 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.615A pdb=" N TYR I 64 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS I 22 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 62 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.598A pdb=" N TYR J 65 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.506A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.537A pdb=" N LEU N 74 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU N 79 " --> pdb=" O LEU N 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'S' and resid 31 through 32 removed outlier: 6.369A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1212 hydrogen bonds 1892 hydrogen bond angles 0 basepair planarities 486 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 32.07 Time building geometry restraints manager: 10.30 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: 4704 1.31 - 1.44: 23061 1.44 - 1.56: 21420 1.56 - 1.69: 3048 1.69 - 1.81: 95 Bond restraints: 52328 Sorted by residual: bond pdb=" CA GLN H 4 " pdb=" C GLN H 4 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.28e-02 6.10e+03 3.73e+01 bond pdb=" CA ALA S 75 " pdb=" C ALA S 75 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.26e-02 6.30e+03 3.10e+01 bond pdb=" CA ARG L 86 " pdb=" C ARG L 86 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.17e+01 bond pdb=" N ARG N 9 " pdb=" CA ARG N 9 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.18e-02 7.18e+03 1.97e+01 bond pdb=" CA GLU T 15 " pdb=" C GLU T 15 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.16e-02 7.43e+03 1.93e+01 ... (remaining 52323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 77287 2.99 - 5.98: 815 5.98 - 8.97: 87 8.97 - 11.96: 14 11.96 - 14.95: 7 Bond angle restraints: 78210 Sorted by residual: angle pdb=" O3' C A 930 " pdb=" P C A 931 " pdb=" O5' C A 931 " ideal model delta sigma weight residual 104.00 118.95 -14.95 1.50e+00 4.44e-01 9.93e+01 angle pdb=" O3' G A 925 " pdb=" C3' G A 925 " pdb=" C2' G A 925 " ideal model delta sigma weight residual 109.50 123.85 -14.35 1.50e+00 4.44e-01 9.15e+01 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 115.08 100.95 14.13 1.64e+00 3.72e-01 7.42e+01 angle pdb=" N PHE C 130 " pdb=" CA PHE C 130 " pdb=" C PHE C 130 " ideal model delta sigma weight residual 111.71 120.22 -8.51 1.15e+00 7.56e-01 5.48e+01 angle pdb=" N HIS K 24 " pdb=" CA HIS K 24 " pdb=" C HIS K 24 " ideal model delta sigma weight residual 109.96 99.66 10.30 1.50e+00 4.44e-01 4.71e+01 ... (remaining 78205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 29903 35.98 - 71.97: 3274 71.97 - 107.95: 369 107.95 - 143.94: 13 143.94 - 179.92: 13 Dihedral angle restraints: 33572 sinusoidal: 27946 harmonic: 5626 Sorted by residual: dihedral pdb=" O4' C A1028 " pdb=" C1' C A1028 " pdb=" N1 C A1028 " pdb=" C2 C A1028 " ideal model delta sinusoidal sigma weight residual 200.00 37.05 162.95 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 39.84 160.16 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U A1030 " pdb=" C1' U A1030 " pdb=" N1 U A1030 " pdb=" C2 U A1030 " ideal model delta sinusoidal sigma weight residual 200.00 44.80 155.20 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 33569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 9901 0.179 - 0.358: 71 0.358 - 0.537: 3 0.537 - 0.716: 1 0.716 - 0.895: 1 Chirality restraints: 9977 Sorted by residual: chirality pdb=" C3' G A 925 " pdb=" C4' G A 925 " pdb=" O3' G A 925 " pdb=" C2' G A 925 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C3' G A1392 " pdb=" C4' G A1392 " pdb=" O3' G A1392 " pdb=" C2' G A1392 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" C4' G A1392 " pdb=" C5' G A1392 " pdb=" O4' G A1392 " pdb=" C3' G A1392 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 9974 not shown) Planarity restraints: 4250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 876 " -0.034 2.00e-02 2.50e+03 3.64e-02 2.98e+01 pdb=" N1 C A 876 " 0.086 2.00e-02 2.50e+03 pdb=" C2 C A 876 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C A 876 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C A 876 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C A 876 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C A 876 " -0.000 2.00e-02 2.50e+03 pdb=" C5 C A 876 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C A 876 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 854 " 0.028 2.00e-02 2.50e+03 3.53e-02 2.80e+01 pdb=" N1 U A 854 " -0.082 2.00e-02 2.50e+03 pdb=" C2 U A 854 " 0.056 2.00e-02 2.50e+03 pdb=" O2 U A 854 " -0.014 2.00e-02 2.50e+03 pdb=" N3 U A 854 " -0.008 2.00e-02 2.50e+03 pdb=" C4 U A 854 " 0.000 2.00e-02 2.50e+03 pdb=" O4 U A 854 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U A 854 " 0.010 2.00e-02 2.50e+03 pdb=" C6 U A 854 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 795 " -0.030 2.00e-02 2.50e+03 3.46e-02 2.69e+01 pdb=" N1 C A 795 " 0.082 2.00e-02 2.50e+03 pdb=" C2 C A 795 " -0.052 2.00e-02 2.50e+03 pdb=" O2 C A 795 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C A 795 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C A 795 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C A 795 " 0.001 2.00e-02 2.50e+03 pdb=" C5 C A 795 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C A 795 " -0.011 2.00e-02 2.50e+03 ... (remaining 4247 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 21 2.15 - 2.84: 14585 2.84 - 3.52: 67864 3.52 - 4.21: 139649 4.21 - 4.90: 191729 Nonbonded interactions: 413848 Sorted by model distance: nonbonded pdb=" O6 G A 927 " pdb=" O2 U A1390 " model vdw 1.460 2.432 nonbonded pdb=" C6 U A 789 " pdb=" O2' G A 791 " model vdw 1.584 3.340 nonbonded pdb=" N3 U A 789 " pdb=" N7 A A 792 " model vdw 1.683 3.200 nonbonded pdb=" O4 U A 789 " pdb=" N3 G A 791 " model vdw 1.715 3.120 nonbonded pdb=" C5 U A 789 " pdb=" C1' G A 791 " model vdw 1.872 3.770 ... (remaining 413843 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.040 Extract box with map and model: 1.590 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 101.460 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 52328 Z= 0.324 Angle : 0.810 14.948 78210 Z= 0.464 Chirality : 0.048 0.895 9977 Planarity : 0.007 0.119 4250 Dihedral : 22.921 179.923 29940 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.94 % Favored : 92.49 % Rotamer: Outliers : 1.29 % Allowed : 25.37 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1931 helix: -0.84 (0.19), residues: 670 sheet: -0.83 (0.27), residues: 350 loop : -1.95 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 34 HIS 0.019 0.001 HIS F 3 PHE 0.030 0.002 PHE C 130 TYR 0.036 0.002 TYR O 78 ARG 0.016 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 461 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 GLU cc_start: 0.8349 (tp30) cc_final: 0.8108 (mm-30) REVERT: D 206 LYS cc_start: 0.8175 (ptmm) cc_final: 0.7853 (ttpt) REVERT: E 65 GLU cc_start: 0.8574 (tp30) cc_final: 0.7584 (tp30) REVERT: E 77 ASN cc_start: 0.8849 (t0) cc_final: 0.8494 (t0) REVERT: E 86 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8573 (tttt) REVERT: F 90 MET cc_start: 0.7917 (ttp) cc_final: 0.7338 (tpt) REVERT: H 5 ASP cc_start: 0.8732 (t0) cc_final: 0.8394 (t0) REVERT: H 48 ASP cc_start: 0.8656 (t0) cc_final: 0.8262 (t0) REVERT: L 76 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8165 (mm-30) REVERT: L 112 GLN cc_start: 0.8209 (mt0) cc_final: 0.7761 (mt0) REVERT: O 47 LYS cc_start: 0.8420 (ptmm) cc_final: 0.8120 (tmtt) REVERT: O 72 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7754 (ttp80) REVERT: P 8 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7888 (ttt-90) REVERT: Q 5 ILE cc_start: 0.8718 (tt) cc_final: 0.8472 (pt) REVERT: Q 40 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8414 (mmm160) REVERT: C 20 SER cc_start: 0.8351 (t) cc_final: 0.8125 (p) REVERT: C 140 ASN cc_start: 0.8184 (m-40) cc_final: 0.7670 (m-40) REVERT: C 154 SER cc_start: 0.8391 (p) cc_final: 0.8095 (m) REVERT: I 94 LEU cc_start: 0.7610 (mm) cc_final: 0.7126 (mp) REVERT: M 76 SER cc_start: 0.7891 (p) cc_final: 0.7677 (p) REVERT: N 82 ILE cc_start: 0.8376 (pt) cc_final: 0.7928 (mt) REVERT: N 92 GLU cc_start: 0.7350 (mp0) cc_final: 0.7086 (mp0) REVERT: S 39 THR cc_start: 0.6140 (m) cc_final: 0.5875 (p) outliers start: 21 outliers final: 5 residues processed: 475 average time/residue: 0.5523 time to fit residues: 411.3360 Evaluate side-chains 348 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 342 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain N residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.9980 chunk 257 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 HIS F 17 GLN F 58 HIS H 118 GLN K 81 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN T 70 ASN T 82 GLN I 32 GLN S 56 GLN S 57 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 52328 Z= 0.315 Angle : 0.681 9.241 78210 Z= 0.348 Chirality : 0.039 0.306 9977 Planarity : 0.006 0.067 4250 Dihedral : 23.002 178.107 26042 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 4.25 % Allowed : 20.75 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1931 helix: 0.11 (0.19), residues: 704 sheet: -0.42 (0.27), residues: 353 loop : -1.30 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 201 HIS 0.008 0.002 HIS S 52 PHE 0.016 0.002 PHE P 16 TYR 0.027 0.002 TYR F 25 ARG 0.007 0.001 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 349 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7799 (mmm-85) REVERT: E 65 GLU cc_start: 0.8589 (tp30) cc_final: 0.7983 (tp30) REVERT: E 69 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7865 (ptp90) REVERT: E 86 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8409 (tttt) REVERT: F 90 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7438 (tpp) REVERT: H 43 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7782 (mm-30) REVERT: H 47 GLU cc_start: 0.8191 (tp30) cc_final: 0.7812 (tp30) REVERT: H 48 ASP cc_start: 0.8592 (t0) cc_final: 0.8350 (t0) REVERT: H 58 GLU cc_start: 0.7650 (mp0) cc_final: 0.7383 (mp0) REVERT: K 53 ARG cc_start: 0.6376 (mmp80) cc_final: 0.6152 (mmm160) REVERT: L 70 GLU cc_start: 0.7705 (pm20) cc_final: 0.7313 (pm20) REVERT: L 76 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8166 (mm-30) REVERT: L 112 GLN cc_start: 0.8169 (mt0) cc_final: 0.7850 (mt0) REVERT: O 38 HIS cc_start: 0.6761 (t70) cc_final: 0.6523 (t-170) REVERT: O 72 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7929 (ttp80) REVERT: P 48 GLU cc_start: 0.7239 (tt0) cc_final: 0.7006 (tt0) REVERT: Q 40 ARG cc_start: 0.9098 (mmm-85) cc_final: 0.8387 (mmm160) REVERT: R 32 TYR cc_start: 0.6861 (m-80) cc_final: 0.6546 (m-80) REVERT: T 53 GLU cc_start: 0.8790 (pp20) cc_final: 0.8573 (pp20) REVERT: C 20 SER cc_start: 0.8718 (t) cc_final: 0.8084 (p) REVERT: C 142 MET cc_start: 0.8078 (mmm) cc_final: 0.7709 (mmm) REVERT: C 149 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8628 (mp) REVERT: C 152 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7557 (tm-30) REVERT: J 71 LEU cc_start: 0.6884 (mt) cc_final: 0.6503 (mt) REVERT: M 91 HIS cc_start: 0.6119 (OUTLIER) cc_final: 0.5775 (t-90) REVERT: N 82 ILE cc_start: 0.8319 (pt) cc_final: 0.7946 (mt) REVERT: N 92 GLU cc_start: 0.7625 (mp0) cc_final: 0.7038 (mp0) outliers start: 69 outliers final: 38 residues processed: 394 average time/residue: 0.5119 time to fit residues: 325.7743 Evaluate side-chains 354 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 256 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 52328 Z= 0.381 Angle : 0.710 8.606 78210 Z= 0.363 Chirality : 0.041 0.260 9977 Planarity : 0.006 0.060 4250 Dihedral : 23.062 178.944 26031 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 5.91 % Allowed : 20.20 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1931 helix: 0.38 (0.19), residues: 696 sheet: -0.44 (0.27), residues: 368 loop : -1.28 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 201 HIS 0.008 0.002 HIS O 51 PHE 0.019 0.002 PHE S 41 TYR 0.019 0.002 TYR M 23 ARG 0.010 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 345 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7736 (mt) REVERT: D 206 LYS cc_start: 0.8222 (ptmm) cc_final: 0.7958 (ttpt) REVERT: E 54 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7905 (mmm-85) REVERT: E 61 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8235 (tp-100) REVERT: E 65 GLU cc_start: 0.8645 (tp30) cc_final: 0.8140 (tp30) REVERT: E 69 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7939 (ptp90) REVERT: E 116 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7989 (tm-30) REVERT: F 3 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6524 (m-70) REVERT: F 90 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7646 (tpp) REVERT: H 48 ASP cc_start: 0.8555 (t0) cc_final: 0.8244 (t0) REVERT: H 73 GLU cc_start: 0.7587 (mp0) cc_final: 0.7202 (mp0) REVERT: H 87 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8974 (mmtp) REVERT: K 56 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7410 (tpt90) REVERT: L 70 GLU cc_start: 0.7791 (pm20) cc_final: 0.7506 (pm20) REVERT: L 76 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8277 (mm-30) REVERT: L 112 GLN cc_start: 0.8366 (mt0) cc_final: 0.7967 (mt0) REVERT: Q 40 ARG cc_start: 0.9152 (mmm-85) cc_final: 0.8477 (mmm160) REVERT: Q 81 LYS cc_start: 0.9161 (tppt) cc_final: 0.8956 (mmmt) REVERT: C 20 SER cc_start: 0.8810 (t) cc_final: 0.8004 (p) REVERT: C 36 ASP cc_start: 0.8974 (t0) cc_final: 0.8610 (t0) REVERT: C 142 MET cc_start: 0.8026 (mmm) cc_final: 0.7769 (mmm) REVERT: C 149 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8934 (mp) REVERT: C 185 ASN cc_start: 0.8770 (m-40) cc_final: 0.8478 (m-40) REVERT: C 204 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8899 (mtmm) REVERT: I 61 LEU cc_start: 0.7956 (mt) cc_final: 0.7751 (mt) REVERT: I 100 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8011 (mmtm) REVERT: M 91 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.5918 (t-90) REVERT: N 82 ILE cc_start: 0.8510 (pt) cc_final: 0.8131 (mt) REVERT: N 92 GLU cc_start: 0.7578 (mp0) cc_final: 0.6789 (mp0) REVERT: S 70 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7670 (mmmm) outliers start: 96 outliers final: 64 residues processed: 401 average time/residue: 0.5115 time to fit residues: 333.5504 Evaluate side-chains 386 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN F 58 HIS ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS C 139 GLN N 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 52328 Z= 0.237 Angle : 0.594 8.254 78210 Z= 0.306 Chirality : 0.036 0.255 9977 Planarity : 0.005 0.056 4250 Dihedral : 22.911 179.902 26029 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 5.42 % Allowed : 21.49 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1931 helix: 0.63 (0.20), residues: 703 sheet: -0.30 (0.27), residues: 373 loop : -1.12 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.007 0.001 HIS O 38 PHE 0.013 0.002 PHE P 16 TYR 0.017 0.002 TYR I 90 ARG 0.009 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 MET cc_start: 0.8072 (mtp) cc_final: 0.7744 (mtp) REVERT: D 190 ASP cc_start: 0.8086 (m-30) cc_final: 0.6968 (m-30) REVERT: E 54 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7926 (mmm-85) REVERT: E 61 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8194 (tp-100) REVERT: E 65 GLU cc_start: 0.8634 (tp30) cc_final: 0.8132 (tp30) REVERT: E 78 ASN cc_start: 0.8641 (p0) cc_final: 0.8388 (p0) REVERT: E 116 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8012 (tm-30) REVERT: F 3 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: F 90 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: H 48 ASP cc_start: 0.8556 (t0) cc_final: 0.8224 (t0) REVERT: H 73 GLU cc_start: 0.7562 (mp0) cc_final: 0.7186 (mp0) REVERT: H 76 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7526 (mm110) REVERT: K 56 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7587 (tmt-80) REVERT: L 70 GLU cc_start: 0.7803 (pm20) cc_final: 0.7550 (pm20) REVERT: L 112 GLN cc_start: 0.8106 (mt0) cc_final: 0.7765 (mt0) REVERT: Q 40 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8458 (mmm160) REVERT: Q 81 LYS cc_start: 0.9168 (tppt) cc_final: 0.8956 (mmmt) REVERT: T 60 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8040 (ttp80) REVERT: C 20 SER cc_start: 0.8790 (t) cc_final: 0.7995 (p) REVERT: C 36 ASP cc_start: 0.8931 (t0) cc_final: 0.8555 (t0) REVERT: C 142 MET cc_start: 0.8013 (mmm) cc_final: 0.7781 (mmm) REVERT: C 149 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8964 (mp) REVERT: C 185 ASN cc_start: 0.8759 (m-40) cc_final: 0.8465 (m-40) REVERT: C 204 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8864 (mtmm) REVERT: I 100 LYS cc_start: 0.8352 (ptpp) cc_final: 0.7957 (mmtm) REVERT: M 91 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5898 (t-90) REVERT: N 5 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8122 (p) REVERT: N 82 ILE cc_start: 0.8387 (pt) cc_final: 0.7982 (mt) outliers start: 88 outliers final: 61 residues processed: 386 average time/residue: 0.4921 time to fit residues: 311.8871 Evaluate side-chains 380 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 38 HIS Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN S 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 52328 Z= 0.136 Angle : 0.523 12.329 78210 Z= 0.270 Chirality : 0.032 0.302 9977 Planarity : 0.004 0.053 4250 Dihedral : 22.811 178.785 26029 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 4.13 % Allowed : 23.77 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1931 helix: 0.95 (0.20), residues: 692 sheet: -0.13 (0.27), residues: 371 loop : -0.92 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 22 HIS 0.018 0.001 HIS O 38 PHE 0.012 0.001 PHE F 8 TYR 0.015 0.001 TYR I 90 ARG 0.011 0.000 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 336 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 ILE cc_start: 0.8795 (pt) cc_final: 0.8506 (mm) REVERT: D 124 MET cc_start: 0.7988 (mtp) cc_final: 0.7691 (mtp) REVERT: D 190 ASP cc_start: 0.7876 (m-30) cc_final: 0.7638 (m-30) REVERT: E 54 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7982 (mmm-85) REVERT: E 61 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8170 (tp-100) REVERT: E 65 GLU cc_start: 0.8572 (tp30) cc_final: 0.7947 (tp30) REVERT: E 78 ASN cc_start: 0.8645 (p0) cc_final: 0.8389 (p0) REVERT: E 86 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8179 (tttt) REVERT: E 116 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7892 (tm-30) REVERT: E 156 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8203 (ttpp) REVERT: F 3 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6637 (m-70) REVERT: F 90 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: H 48 ASP cc_start: 0.8493 (t0) cc_final: 0.8062 (t0) REVERT: H 73 GLU cc_start: 0.7549 (mp0) cc_final: 0.7022 (mp0) REVERT: H 76 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7506 (mm110) REVERT: K 24 HIS cc_start: 0.6734 (t70) cc_final: 0.6508 (t70) REVERT: K 56 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7573 (tpt170) REVERT: L 66 TYR cc_start: 0.8840 (t80) cc_final: 0.8612 (t80) REVERT: L 112 GLN cc_start: 0.7748 (mt0) cc_final: 0.7464 (mt0) REVERT: Q 40 ARG cc_start: 0.9106 (mmm-85) cc_final: 0.8399 (mmm160) REVERT: C 22 TRP cc_start: 0.8731 (p-90) cc_final: 0.8356 (p-90) REVERT: C 36 ASP cc_start: 0.8888 (t0) cc_final: 0.8523 (t0) REVERT: C 149 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8981 (mp) REVERT: C 185 ASN cc_start: 0.8755 (m-40) cc_final: 0.8402 (m-40) REVERT: C 204 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8834 (mtmm) REVERT: I 100 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7922 (mmtm) REVERT: M 91 HIS cc_start: 0.6418 (OUTLIER) cc_final: 0.5850 (t-90) REVERT: N 5 SER cc_start: 0.8318 (m) cc_final: 0.8118 (p) REVERT: N 82 ILE cc_start: 0.8320 (pt) cc_final: 0.7905 (tp) outliers start: 67 outliers final: 44 residues processed: 381 average time/residue: 0.4934 time to fit residues: 309.0537 Evaluate side-chains 359 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.6980 chunk 295 optimal weight: 0.2980 chunk 64 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 80 GLN P 59 HIS T 13 GLN T 48 GLN C 139 GLN I 81 HIS ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52328 Z= 0.193 Angle : 0.547 8.999 78210 Z= 0.282 Chirality : 0.033 0.297 9977 Planarity : 0.004 0.052 4250 Dihedral : 22.784 177.867 26029 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 5.60 % Allowed : 22.84 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1931 helix: 0.90 (0.20), residues: 711 sheet: -0.20 (0.27), residues: 373 loop : -0.92 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS S 52 PHE 0.013 0.001 PHE C 203 TYR 0.013 0.001 TYR D 51 ARG 0.011 0.000 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 313 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 ILE cc_start: 0.8723 (pt) cc_final: 0.8442 (mm) REVERT: D 124 MET cc_start: 0.8034 (mtp) cc_final: 0.7833 (mtp) REVERT: D 190 ASP cc_start: 0.7843 (m-30) cc_final: 0.7547 (m-30) REVERT: E 54 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7965 (mmm-85) REVERT: E 61 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8215 (tp-100) REVERT: E 65 GLU cc_start: 0.8622 (tp30) cc_final: 0.8018 (tp30) REVERT: E 116 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7960 (tm-30) REVERT: F 3 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6608 (m-70) REVERT: F 90 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7782 (tpp) REVERT: H 47 GLU cc_start: 0.8170 (tp30) cc_final: 0.7824 (tp30) REVERT: H 48 ASP cc_start: 0.8507 (t0) cc_final: 0.8270 (t0) REVERT: H 73 GLU cc_start: 0.7539 (mp0) cc_final: 0.7135 (mp0) REVERT: L 66 TYR cc_start: 0.8875 (t80) cc_final: 0.8607 (t80) REVERT: L 112 GLN cc_start: 0.7942 (mt0) cc_final: 0.7663 (mt0) REVERT: Q 40 ARG cc_start: 0.9122 (mmm-85) cc_final: 0.8416 (mmm160) REVERT: T 60 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8257 (ttp80) REVERT: C 21 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8530 (t) REVERT: C 36 ASP cc_start: 0.8904 (t0) cc_final: 0.8533 (t0) REVERT: C 149 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8983 (mp) REVERT: C 204 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8753 (mtmm) REVERT: I 100 LYS cc_start: 0.8331 (ptpp) cc_final: 0.7948 (mmtm) REVERT: J 24 GLU cc_start: 0.7608 (pp20) cc_final: 0.7386 (pp20) REVERT: M 91 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5900 (t-90) REVERT: N 73 PHE cc_start: 0.8141 (t80) cc_final: 0.7668 (t80) REVERT: N 82 ILE cc_start: 0.8408 (pt) cc_final: 0.8017 (mt) outliers start: 91 outliers final: 68 residues processed: 370 average time/residue: 0.4874 time to fit residues: 299.0084 Evaluate side-chains 381 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN E 97 GLN E 135 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 38 HIS T 13 GLN C 139 GLN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 52328 Z= 0.466 Angle : 0.776 9.178 78210 Z= 0.392 Chirality : 0.044 0.281 9977 Planarity : 0.006 0.074 4250 Dihedral : 23.072 178.516 26029 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 6.47 % Allowed : 23.15 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1931 helix: 0.38 (0.19), residues: 706 sheet: -0.50 (0.27), residues: 371 loop : -1.12 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 34 HIS 0.010 0.002 HIS O 51 PHE 0.020 0.002 PHE D 182 TYR 0.022 0.002 TYR R 64 ARG 0.013 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 312 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 ASP cc_start: 0.7612 (t70) cc_final: 0.7399 (t70) REVERT: D 185 LYS cc_start: 0.9511 (mtpt) cc_final: 0.9269 (mtpp) REVERT: D 190 ASP cc_start: 0.7770 (m-30) cc_final: 0.7415 (m-30) REVERT: E 54 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7965 (mmm-85) REVERT: E 61 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8180 (tp-100) REVERT: E 65 GLU cc_start: 0.8642 (tp30) cc_final: 0.8099 (tp30) REVERT: E 116 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8144 (tm-30) REVERT: F 3 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6462 (m-70) REVERT: H 47 GLU cc_start: 0.8259 (tp30) cc_final: 0.7889 (tp30) REVERT: H 48 ASP cc_start: 0.8584 (t0) cc_final: 0.8268 (t0) REVERT: H 73 GLU cc_start: 0.7515 (mp0) cc_final: 0.7121 (mp0) REVERT: H 76 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7509 (mm110) REVERT: H 87 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (mmtp) REVERT: K 68 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8319 (mm-30) REVERT: L 112 GLN cc_start: 0.8380 (mt0) cc_final: 0.7932 (mt0) REVERT: Q 40 ARG cc_start: 0.9132 (mmm-85) cc_final: 0.8465 (mmm160) REVERT: T 60 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7895 (ttp80) REVERT: C 36 ASP cc_start: 0.8935 (t0) cc_final: 0.8582 (t0) REVERT: C 149 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8962 (mp) REVERT: C 185 ASN cc_start: 0.8724 (m-40) cc_final: 0.8496 (m-40) REVERT: C 204 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8761 (mtmm) REVERT: I 100 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8116 (mmtm) REVERT: M 81 MET cc_start: 0.8204 (mmm) cc_final: 0.7642 (tpp) REVERT: M 91 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.5858 (t-90) REVERT: M 93 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.6016 (mpp80) REVERT: N 73 PHE cc_start: 0.8354 (t80) cc_final: 0.7689 (t80) REVERT: N 82 ILE cc_start: 0.8558 (pt) cc_final: 0.8334 (mt) outliers start: 105 outliers final: 72 residues processed: 385 average time/residue: 0.4923 time to fit residues: 311.7786 Evaluate side-chains 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 30.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 52328 Z= 0.285 Angle : 0.634 10.978 78210 Z= 0.325 Chirality : 0.038 0.280 9977 Planarity : 0.005 0.061 4250 Dihedral : 22.914 179.604 26029 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 4.99 % Allowed : 25.12 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1931 helix: 0.48 (0.19), residues: 710 sheet: -0.46 (0.27), residues: 370 loop : -1.09 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.005 0.001 HIS O 51 PHE 0.013 0.001 PHE D 182 TYR 0.022 0.002 TYR C 193 ARG 0.012 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.7872 (m-30) cc_final: 0.7510 (m-30) REVERT: E 54 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7969 (mmm-85) REVERT: E 61 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8184 (tp-100) REVERT: E 65 GLU cc_start: 0.8622 (tp30) cc_final: 0.8066 (tp30) REVERT: E 116 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 3 HIS cc_start: 0.6839 (OUTLIER) cc_final: 0.6401 (m-70) REVERT: F 90 MET cc_start: 0.8086 (mtp) cc_final: 0.7721 (tpt) REVERT: H 47 GLU cc_start: 0.8302 (tp30) cc_final: 0.7932 (tp30) REVERT: H 48 ASP cc_start: 0.8555 (t0) cc_final: 0.8238 (t0) REVERT: H 73 GLU cc_start: 0.7541 (mp0) cc_final: 0.7144 (mp0) REVERT: L 66 TYR cc_start: 0.8873 (t80) cc_final: 0.8610 (t80) REVERT: L 112 GLN cc_start: 0.8214 (mt0) cc_final: 0.7770 (mt0) REVERT: Q 40 ARG cc_start: 0.9102 (mmm-85) cc_final: 0.8463 (mmm160) REVERT: T 60 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: C 36 ASP cc_start: 0.8921 (t0) cc_final: 0.8562 (t0) REVERT: C 149 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9001 (mp) REVERT: C 150 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7894 (ptmm) REVERT: C 185 ASN cc_start: 0.8722 (m-40) cc_final: 0.8481 (m-40) REVERT: C 204 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8725 (mtmm) REVERT: I 100 LYS cc_start: 0.8349 (ptpp) cc_final: 0.8054 (mmtm) REVERT: M 81 MET cc_start: 0.7875 (mmm) cc_final: 0.7492 (tpp) REVERT: M 91 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.5419 (t-90) REVERT: M 93 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5948 (tpp80) REVERT: N 73 PHE cc_start: 0.8302 (t80) cc_final: 0.7629 (t80) REVERT: N 82 ILE cc_start: 0.8531 (pt) cc_final: 0.8273 (mt) REVERT: S 32 ARG cc_start: 0.5125 (ttp80) cc_final: 0.4854 (ttp-170) outliers start: 81 outliers final: 64 residues processed: 375 average time/residue: 0.5023 time to fit residues: 307.7130 Evaluate side-chains 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 315 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS K 64 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 52328 Z= 0.364 Angle : 0.683 10.944 78210 Z= 0.349 Chirality : 0.040 0.276 9977 Planarity : 0.005 0.063 4250 Dihedral : 22.950 179.361 26029 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 5.23 % Allowed : 25.37 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1931 helix: 0.37 (0.19), residues: 709 sheet: -0.54 (0.27), residues: 368 loop : -1.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 201 HIS 0.006 0.001 HIS O 51 PHE 0.016 0.002 PHE D 182 TYR 0.022 0.002 TYR C 193 ARG 0.013 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 315 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 185 LYS cc_start: 0.9489 (mtpt) cc_final: 0.9271 (mtpp) REVERT: D 190 ASP cc_start: 0.7851 (m-30) cc_final: 0.7479 (m-30) REVERT: D 206 LYS cc_start: 0.8277 (ptmm) cc_final: 0.7995 (ttpt) REVERT: E 54 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7941 (mmm-85) REVERT: E 61 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8185 (tp-100) REVERT: E 65 GLU cc_start: 0.8625 (tp30) cc_final: 0.8129 (tp30) REVERT: E 116 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8099 (tm-30) REVERT: F 3 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6370 (m-70) REVERT: F 90 MET cc_start: 0.8141 (mtp) cc_final: 0.7799 (tpt) REVERT: H 47 GLU cc_start: 0.8327 (tp30) cc_final: 0.7987 (tp30) REVERT: H 48 ASP cc_start: 0.8591 (t0) cc_final: 0.8292 (t0) REVERT: H 73 GLU cc_start: 0.7542 (mp0) cc_final: 0.7145 (mp0) REVERT: H 76 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7518 (mm110) REVERT: H 87 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8993 (mmtp) REVERT: L 112 GLN cc_start: 0.8306 (mt0) cc_final: 0.7855 (mt0) REVERT: Q 40 ARG cc_start: 0.9112 (mmm-85) cc_final: 0.8472 (mmm160) REVERT: T 60 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: C 36 ASP cc_start: 0.8927 (t0) cc_final: 0.8289 (m-30) REVERT: C 149 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 150 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7928 (ptmm) REVERT: C 185 ASN cc_start: 0.8718 (m-40) cc_final: 0.8504 (m-40) REVERT: C 204 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8748 (mtmm) REVERT: I 100 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8067 (mmtm) REVERT: M 91 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.5559 (t-90) REVERT: M 92 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.8054 (mmt-90) REVERT: M 93 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5866 (tpp80) REVERT: N 73 PHE cc_start: 0.8349 (t80) cc_final: 0.7630 (t80) REVERT: N 82 ILE cc_start: 0.8603 (pt) cc_final: 0.8359 (mt) REVERT: S 32 ARG cc_start: 0.5136 (ttp80) cc_final: 0.4911 (ttp-170) outliers start: 85 outliers final: 66 residues processed: 375 average time/residue: 0.5198 time to fit residues: 318.6670 Evaluate side-chains 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 7.9990 chunk 322 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 0.0030 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 4.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 52328 Z= 0.276 Angle : 0.624 11.204 78210 Z= 0.321 Chirality : 0.037 0.286 9977 Planarity : 0.005 0.061 4250 Dihedral : 22.902 178.894 26029 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.56 % Allowed : 25.99 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1931 helix: 0.49 (0.19), residues: 709 sheet: -0.53 (0.27), residues: 370 loop : -1.07 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS O 51 PHE 0.014 0.001 PHE D 182 TYR 0.023 0.002 TYR C 193 ARG 0.014 0.001 ARG I 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 185 LYS cc_start: 0.9475 (mtpt) cc_final: 0.9251 (mtpp) REVERT: D 190 ASP cc_start: 0.7912 (m-30) cc_final: 0.7575 (m-30) REVERT: E 54 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7923 (mmm-85) REVERT: E 61 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8169 (tp-100) REVERT: E 65 GLU cc_start: 0.8607 (tp30) cc_final: 0.8016 (tp30) REVERT: E 116 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8080 (tm-30) REVERT: F 3 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6421 (m-70) REVERT: F 90 MET cc_start: 0.8083 (mtp) cc_final: 0.7667 (mmm) REVERT: H 47 GLU cc_start: 0.8332 (tp30) cc_final: 0.8061 (tp30) REVERT: H 48 ASP cc_start: 0.8597 (t0) cc_final: 0.8296 (t0) REVERT: H 73 GLU cc_start: 0.7532 (mp0) cc_final: 0.7215 (mp0) REVERT: H 76 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7500 (mm110) REVERT: H 87 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8975 (mmtp) REVERT: L 66 TYR cc_start: 0.8850 (t80) cc_final: 0.8591 (t80) REVERT: L 112 GLN cc_start: 0.8182 (mt0) cc_final: 0.7763 (mt0) REVERT: Q 40 ARG cc_start: 0.9097 (mmm-85) cc_final: 0.8469 (mmm160) REVERT: T 60 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: C 36 ASP cc_start: 0.8915 (t0) cc_final: 0.8285 (m-30) REVERT: C 149 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9010 (mp) REVERT: C 150 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7906 (ptmm) REVERT: C 204 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8649 (mttt) REVERT: I 100 LYS cc_start: 0.8327 (ptpp) cc_final: 0.8088 (mmtm) REVERT: I 126 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7963 (mm-40) REVERT: M 81 MET cc_start: 0.7866 (tpt) cc_final: 0.7507 (tpp) REVERT: N 73 PHE cc_start: 0.8295 (t80) cc_final: 0.7627 (t80) REVERT: N 82 ILE cc_start: 0.8489 (pt) cc_final: 0.8234 (mt) outliers start: 74 outliers final: 64 residues processed: 367 average time/residue: 0.5106 time to fit residues: 305.5258 Evaluate side-chains 378 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 309 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 20.0000 chunk 287 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 270 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN T 13 GLN C 139 GLN J 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058150 restraints weight = 162537.879| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.13 r_work: 0.2859 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 52328 Z= 0.224 Angle : 0.588 10.415 78210 Z= 0.305 Chirality : 0.035 0.294 9977 Planarity : 0.005 0.059 4250 Dihedral : 22.867 178.803 26029 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 4.56 % Allowed : 25.86 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1931 helix: 0.61 (0.19), residues: 708 sheet: -0.48 (0.27), residues: 369 loop : -0.99 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS K 24 PHE 0.012 0.001 PHE F 8 TYR 0.021 0.002 TYR C 193 ARG 0.014 0.001 ARG I 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8515.61 seconds wall clock time: 150 minutes 51.57 seconds (9051.57 seconds total)