Starting phenix.real_space_refine on Fri Nov 21 03:58:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xyu_6790/11_2025/5xyu_6790.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1379 5.49 5 Mg 48 5.21 5 S 32 5.16 5 C 22881 2.51 5 N 8466 2.21 5 O 12351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45157 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 29639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 29639 Classifications: {'RNA': 1379} Modifications used: {'rna2p_pur': 116, 'rna2p_pyr': 90, 'rna3p_pur': 674, 'rna3p_pyr': 499} Link IDs: {'rna2p': 206, 'rna3p': 1172} Chain breaks: 16 Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 3 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1156 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 4 Chain: "E" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1147 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "G" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain breaks: 2 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 990 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 974 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 778 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain breaks: 1 Chain: "K" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 853 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 964 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 54} Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "P" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 745 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain breaks: 1 Chain: "Q" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 721 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "R" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "S" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "T" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "U" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 217 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Unusual residues: {' MG': 47} Classifications: {'undetermined': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.23, per 1000 atoms: 0.20 Number of scatterers: 45157 At special positions: 0 Unit cell: (154.44, 205.92, 190.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 1379 15.00 Mg 48 11.99 O 12351 8.00 N 8466 7.00 C 22881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 40 " distance=1.84 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 40 " distance=1.83 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=1.24 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 977.3 milliseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 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: 65 helices and 19 sheets defined 41.9% alpha, 14.0% beta 329 base pairs and 743 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.654A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 42 removed outlier: 3.557A pdb=" N ALA C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.542A pdb=" N ALA C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.585A pdb=" N GLN C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.653A pdb=" N ARG C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.200A pdb=" N LEU D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.729A pdb=" N GLU D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.759A pdb=" N LEU D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 86 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.837A pdb=" N GLN D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.690A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.814A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.858A pdb=" N ALA E 138 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.659A pdb=" N VAL E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.642A pdb=" N ALA E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 3.577A pdb=" N VAL F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.832A pdb=" N THR G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.541A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 4.130A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.940A pdb=" N THR G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.556A pdb=" N ILE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.858A pdb=" N ARG G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 30 through 43 removed outlier: 3.694A pdb=" N ALA H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE H 39 " --> pdb=" O ASN H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.651A pdb=" N ARG H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 59 Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.778A pdb=" N GLN I 66 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 67 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 69 " --> pdb=" O GLN I 65 " (cutoff:3.500A) Proline residue: I 71 - end of helix removed outlier: 3.806A pdb=" N VAL I 75 " --> pdb=" O PRO I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 111 removed outlier: 3.669A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU I 109 " --> pdb=" O ARG I 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 122 removed outlier: 3.658A pdb=" N LYS I 120 " --> pdb=" O PRO I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.611A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.574A pdb=" N ASP J 85 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.009A pdb=" N GLY K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 62 through 67 removed outlier: 3.679A pdb=" N ARG K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS K 66 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 81 removed outlier: 4.184A pdb=" N ALA K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN K 73 " --> pdb=" O PRO K 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 removed outlier: 3.640A pdb=" N HIS K 86 " --> pdb=" O LYS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.853A pdb=" N ALA K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'M' and resid 14 through 19 removed outlier: 3.684A pdb=" N LEU M 19 " --> pdb=" O MET M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.865A pdb=" N LEU M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR M 59 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN M 63 " --> pdb=" O TYR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 84 removed outlier: 3.546A pdb=" N GLN M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 83 " --> pdb=" O ARG M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 91 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 4 through 12 removed outlier: 3.538A pdb=" N HIS N 8 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 50 removed outlier: 3.726A pdb=" N ARG N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 removed outlier: 3.927A pdb=" N LYS O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 10 " --> pdb=" O GLU O 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 47 removed outlier: 3.936A pdb=" N ALA O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU O 41 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.650A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.550A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 removed outlier: 3.527A pdb=" N ALA P 72 " --> pdb=" O GLU P 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU P 73 " --> pdb=" O PRO P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.503A pdb=" N LYS P 82 " --> pdb=" O GLY P 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 42 removed outlier: 3.746A pdb=" N LEU R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 57 through 75 removed outlier: 3.509A pdb=" N GLU R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.512A pdb=" N LEU S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU S 24 " --> pdb=" O ASP S 20 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS S 25 " --> pdb=" O VAL S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 removed outlier: 3.769A pdb=" N VAL S 67 " --> pdb=" O GLU S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.047A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.643A pdb=" N ARG T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG T 18 " --> pdb=" O ASN T 14 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA T 38 " --> pdb=" O GLY T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.592A pdb=" N GLU T 49 " --> pdb=" O ASP T 45 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG T 56 " --> pdb=" O HIS T 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP T 59 " --> pdb=" O SER T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 85 removed outlier: 3.503A pdb=" N ALA T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS T 85 " --> pdb=" O LEU T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 19 removed outlier: 3.544A pdb=" N MET U 12 " --> pdb=" O ARG U 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER U 13 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS U 14 " --> pdb=" O LYS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 24 Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.375A pdb=" N ILE C 67 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.542A pdb=" N GLU C 166 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS C 153 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 187 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AA5, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AA6, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.524A pdb=" N ALA E 114 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 151 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 131 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER E 152 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.552A pdb=" N LEU F 8 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 73 through 76 Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.716A pdb=" N ASP H 48 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'H' and resid 77 through 79 removed outlier: 5.809A pdb=" N VAL H 127 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER H 107 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 27 through 28 removed outlier: 3.561A pdb=" N VAL I 42 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.806A pdb=" N GLU J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR J 69 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN J 47 " --> pdb=" O MET J 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 50 through 55 removed outlier: 3.783A pdb=" N ALA K 52 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 91 " --> pdb=" O GLU K 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 36 through 40 removed outlier: 3.700A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 33 through 34 removed outlier: 3.704A pdb=" N LEU N 39 " --> pdb=" O TYR N 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 35 through 36 removed outlier: 3.572A pdb=" N GLU P 35 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL P 3 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 22 through 32 removed outlier: 15.522A pdb=" N THR Q 22 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) removed outlier: 12.305A pdb=" N ARG Q 43 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE Q 24 " --> pdb=" O GLU Q 41 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL Q 37 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP Q 30 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR Q 35 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS Q 44 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LYS Q 86 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS Q 60 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP Q 88 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG Q 87 " --> pdb=" O THR Q 79 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER Q 75 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE Q 93 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG Q 73 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Q 25 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 30 through 33 removed outlier: 3.534A pdb=" N ILE S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 774 hydrogen bonds 1212 hydrogen bond angles 0 basepair planarities 329 basepair parallelities 743 stacking parallelities Total time for adding SS restraints: 20.72 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8902 1.34 - 1.46: 18217 1.46 - 1.58: 18941 1.58 - 1.70: 2740 1.70 - 1.81: 53 Bond restraints: 48853 Sorted by residual: bond pdb=" C ALA E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.30e-02 5.92e+03 2.09e+01 bond pdb=" C LEU M 9 " pdb=" N PRO M 10 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" N PRO F 63 " pdb=" CD PRO F 63 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C HIS E 108 " pdb=" N PRO E 109 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.34e-02 5.57e+03 1.91e+01 bond pdb=" C1' C A1003 " pdb=" N1 C A1003 " ideal model delta sigma weight residual 1.480 1.545 -0.065 1.50e-02 4.44e+03 1.88e+01 ... (remaining 48848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 70794 3.03 - 6.06: 1913 6.06 - 9.09: 49 9.09 - 12.12: 19 12.12 - 15.15: 9 Bond angle restraints: 72784 Sorted by residual: angle pdb=" N HIS E 108 " pdb=" CA HIS E 108 " pdb=" C HIS E 108 " ideal model delta sigma weight residual 108.07 117.25 -9.18 8.90e-01 1.26e+00 1.06e+02 angle pdb=" N ASN M 63 " pdb=" CA ASN M 63 " pdb=" C ASN M 63 " ideal model delta sigma weight residual 111.36 122.04 -10.68 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N LYS J 57 " pdb=" CA LYS J 57 " pdb=" C LYS J 57 " ideal model delta sigma weight residual 113.23 123.24 -10.01 1.22e+00 6.72e-01 6.73e+01 angle pdb=" C4' U A1456 " pdb=" C3' U A1456 " pdb=" O3' U A1456 " ideal model delta sigma weight residual 109.40 121.29 -11.89 1.50e+00 4.44e-01 6.28e+01 angle pdb=" N LYS J 59 " pdb=" CA LYS J 59 " pdb=" C LYS J 59 " ideal model delta sigma weight residual 111.28 119.77 -8.49 1.09e+00 8.42e-01 6.06e+01 ... (remaining 72779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 27638 35.95 - 71.90: 3358 71.90 - 107.85: 439 107.85 - 143.80: 15 143.80 - 179.75: 32 Dihedral angle restraints: 31482 sinusoidal: 25861 harmonic: 5621 Sorted by residual: dihedral pdb=" C5' U A1193 " pdb=" C4' U A1193 " pdb=" C3' U A1193 " pdb=" O3' U A1193 " ideal model delta sinusoidal sigma weight residual 147.00 79.36 67.64 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" C4' U A1193 " pdb=" C3' U A1193 " pdb=" C2' U A1193 " pdb=" C1' U A1193 " ideal model delta sinusoidal sigma weight residual -35.00 30.85 -65.85 1 8.00e+00 1.56e-02 8.86e+01 dihedral pdb=" O4' C A1410 " pdb=" C1' C A1410 " pdb=" N1 C A1410 " pdb=" C2 C A1410 " ideal model delta sinusoidal sigma weight residual 200.00 23.75 176.25 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 31479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 7418 0.127 - 0.253: 1816 0.253 - 0.380: 25 0.380 - 0.507: 7 0.507 - 0.633: 8 Chirality restraints: 9274 Sorted by residual: chirality pdb=" C3' G A 111 " pdb=" C4' G A 111 " pdb=" O3' G A 111 " pdb=" C2' G A 111 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C3' G A 465 " pdb=" C4' G A 465 " pdb=" O3' G A 465 " pdb=" C2' G A 465 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" C3' U A 942 " pdb=" C4' U A 942 " pdb=" O3' U A 942 " pdb=" C2' U A 942 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.15e+00 ... (remaining 9271 not shown) Planarity restraints: 4082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 184 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO E 185 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 185 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 185 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 73 " -0.012 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C LEU F 73 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU F 73 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN F 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 44 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO L 45 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.029 5.00e-02 4.00e+02 ... (remaining 4079 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 61 2.29 - 2.94: 16676 2.94 - 3.59: 67087 3.59 - 4.25: 124985 4.25 - 4.90: 178511 Nonbonded interactions: 387320 Sorted by model distance: nonbonded pdb=" O ASP F 70 " pdb=" ND2 ASN F 74 " model vdw 1.633 3.120 nonbonded pdb=" O ARG M 80 " pdb=" CG1 ILE M 84 " model vdw 1.712 3.440 nonbonded pdb=" O2' U A 939 " pdb=" O5' A A 940 " model vdw 1.783 3.040 nonbonded pdb=" O LYS H 65 " pdb=" OG SER H 73 " model vdw 1.844 3.040 nonbonded pdb=" O2' G A 192 " pdb=" O5' C A 193 " model vdw 1.853 3.040 ... (remaining 387315 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 52.880 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.008 0.794 48857 Z= 0.502 Angle : 1.078 58.518 72790 Z= 0.718 Chirality : 0.097 0.633 9274 Planarity : 0.004 0.088 4082 Dihedral : 24.532 179.748 27841 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 2.26 % Allowed : 6.11 % Favored : 91.63 % Rotamer: Outliers : 1.66 % Allowed : 5.46 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.15), residues: 1900 helix: -2.25 (0.14), residues: 688 sheet: -2.29 (0.24), residues: 330 loop : -2.55 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 126 TYR 0.017 0.001 TYR H 66 PHE 0.014 0.001 PHE C 129 TRP 0.006 0.001 TRP N 61 HIS 0.005 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00632 (48853) covalent geometry : angle 1.04138 (72784) SS BOND : bond 0.48568 ( 3) SS BOND : angle 30.84923 ( 6) hydrogen bonds : bond 0.28555 ( 1374) hydrogen bonds : angle 9.41847 ( 2955) Misc. bond : bond 0.34695 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 645 time to evaluate : 0.873 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: C 36 VAL cc_start: 0.8337 (t) cc_final: 0.8078 (m) REVERT: C 55 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6810 (tt0) REVERT: C 99 GLN cc_start: 0.6320 (mt0) cc_final: 0.5796 (tm-30) REVERT: C 135 LYS cc_start: 0.8324 (mttt) cc_final: 0.8068 (tptp) REVERT: C 142 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6991 (ttp80) REVERT: C 147 LYS cc_start: 0.7610 (tttm) cc_final: 0.7349 (mppt) REVERT: C 188 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 10 ARG cc_start: 0.7517 (ptt-90) cc_final: 0.6285 (tpt170) REVERT: D 17 VAL cc_start: 0.7872 (m) cc_final: 0.7659 (p) REVERT: D 48 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6890 (pm20) REVERT: D 54 GLN cc_start: 0.7877 (tp40) cc_final: 0.7435 (tp40) REVERT: D 91 SER cc_start: 0.8900 (m) cc_final: 0.8628 (p) REVERT: D 99 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6818 (tpt170) REVERT: D 102 LEU cc_start: 0.7914 (tt) cc_final: 0.7708 (mp) REVERT: D 118 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: D 125 VAL cc_start: 0.8982 (t) cc_final: 0.8745 (m) REVERT: D 174 ARG cc_start: 0.6651 (ptm160) cc_final: 0.6349 (mmt-90) REVERT: D 177 VAL cc_start: 0.9003 (t) cc_final: 0.8726 (m) REVERT: E 36 TYR cc_start: 0.7058 (p90) cc_final: 0.6726 (p90) REVERT: E 39 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7208 (ttm110) REVERT: E 75 TYR cc_start: 0.8299 (t80) cc_final: 0.7824 (t80) REVERT: E 91 GLU cc_start: 0.7761 (tp30) cc_final: 0.7317 (tp30) REVERT: E 111 GLN cc_start: 0.8959 (tt0) cc_final: 0.8710 (tt0) REVERT: E 125 SER cc_start: 0.7386 (m) cc_final: 0.7155 (p) REVERT: E 147 ASP cc_start: 0.7764 (m-30) cc_final: 0.7363 (m-30) REVERT: G 9 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7425 (tmtt) REVERT: G 10 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.6743 (mmt180) REVERT: G 58 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.6780 (Cg_exo) REVERT: G 71 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8358 (Cg_exo) REVERT: G 126 ASP cc_start: 0.7951 (m-30) cc_final: 0.7567 (m-30) REVERT: G 136 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7910 (tptt) REVERT: G 140 ASP cc_start: 0.7848 (m-30) cc_final: 0.7273 (m-30) REVERT: H 3 MET cc_start: 0.8307 (mmm) cc_final: 0.8051 (tpp) REVERT: H 31 LYS cc_start: 0.8906 (tptm) cc_final: 0.8582 (ttpt) REVERT: H 38 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8136 (mm-30) REVERT: H 78 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7509 (ptm-80) REVERT: H 115 ASP cc_start: 0.8710 (p0) cc_final: 0.7962 (p0) REVERT: I 61 ASN cc_start: 0.8331 (t0) cc_final: 0.8071 (t0) REVERT: I 107 LEU cc_start: 0.7159 (mt) cc_final: 0.6824 (mt) REVERT: I 115 ARG cc_start: 0.7703 (ttm170) cc_final: 0.7177 (tmt170) REVERT: J 11 LYS cc_start: 0.7532 (mttt) cc_final: 0.7065 (mtpp) REVERT: J 45 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7455 (mt-10) REVERT: J 46 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7533 (ttpt) REVERT: J 47 ASN cc_start: 0.8049 (m-40) cc_final: 0.7722 (m-40) REVERT: J 53 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6854 (mtt180) REVERT: J 71 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7535 (mttm) REVERT: K 32 ILE cc_start: 0.8511 (mp) cc_final: 0.8270 (pt) REVERT: K 41 VAL cc_start: 0.8287 (t) cc_final: 0.7993 (m) REVERT: K 82 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7618 (mttt) REVERT: K 114 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6663 (pp) REVERT: L 3 THR cc_start: 0.8718 (p) cc_final: 0.8470 (p) REVERT: L 6 GLN cc_start: 0.8869 (tt0) cc_final: 0.8569 (tt0) REVERT: L 77 HIS cc_start: 0.8304 (m-70) cc_final: 0.7671 (m90) REVERT: L 87 VAL cc_start: 0.8597 (t) cc_final: 0.8393 (p) REVERT: L 102 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6778 (tt) REVERT: L 105 GLN cc_start: 0.8089 (mt0) cc_final: 0.7791 (mp10) REVERT: L 107 VAL cc_start: 0.8456 (t) cc_final: 0.8187 (m) REVERT: M 16 GLU cc_start: 0.7300 (tt0) cc_final: 0.7069 (tt0) REVERT: M 65 LYS cc_start: 0.7333 (mptt) cc_final: 0.6771 (mmmt) REVERT: M 80 ARG cc_start: 0.7594 (ptt90) cc_final: 0.7377 (tmm-80) REVERT: M 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7154 (tp30) REVERT: M 108 ARG cc_start: 0.5762 (mmt180) cc_final: 0.5410 (mmp-170) REVERT: N 4 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7006 (mtpt) REVERT: N 26 LYS cc_start: 0.7673 (tttp) cc_final: 0.7456 (tttm) REVERT: O 44 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8410 (mtpp) REVERT: O 53 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7623 (mtm-85) REVERT: P 17 GLN cc_start: 0.7687 (mp10) cc_final: 0.6863 (mm-40) REVERT: P 44 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: P 50 GLN cc_start: 0.7656 (mt0) cc_final: 0.6601 (tm-30) REVERT: P 84 LYS cc_start: 0.8514 (tptt) cc_final: 0.8135 (tppt) REVERT: Q 54 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8159 (ttp80) REVERT: Q 77 MET cc_start: 0.8369 (ttm) cc_final: 0.8067 (ttt) REVERT: Q 96 LYS cc_start: 0.8797 (mttm) cc_final: 0.8492 (mmmt) REVERT: R 39 ARG cc_start: 0.8483 (mmt90) cc_final: 0.7931 (mmm-85) REVERT: R 48 ILE cc_start: 0.8452 (mt) cc_final: 0.8131 (mp) REVERT: R 66 VAL cc_start: 0.8709 (t) cc_final: 0.8389 (p) REVERT: S 33 THR cc_start: 0.7922 (m) cc_final: 0.7625 (m) REVERT: T 49 GLU cc_start: 0.8950 (tt0) cc_final: 0.8257 (mt-10) outliers start: 27 outliers final: 10 residues processed: 657 average time/residue: 0.3376 time to fit residues: 336.4834 Evaluate side-chains 516 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 501 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain S residue 29 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 HIS C 68 HIS C 176 HIS ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 25 GLN H 63 GLN H 93 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 75 GLN O 7 GLN O 37 GLN P 15 ASN Q 62 HIS Q 65 ASN R 59 GLN S 29 GLN T 68 HIS T 70 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106391 restraints weight = 85211.791| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.07 r_work: 0.3132 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 48857 Z= 0.146 Angle : 0.692 10.693 72790 Z= 0.357 Chirality : 0.040 0.380 9274 Planarity : 0.005 0.059 4082 Dihedral : 24.819 177.456 23958 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 1.26 % Allowed : 5.47 % Favored : 93.26 % Rotamer: Outliers : 4.17 % Allowed : 12.82 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.17), residues: 1900 helix: -0.32 (0.17), residues: 743 sheet: -1.81 (0.24), residues: 345 loop : -2.21 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 112 TYR 0.014 0.001 TYR H 45 PHE 0.016 0.001 PHE H 10 TRP 0.016 0.001 TRP C 18 HIS 0.018 0.001 HIS S 52 Details of bonding type rmsd covalent geometry : bond 0.00280 (48853) covalent geometry : angle 0.69174 (72784) SS BOND : bond 0.02078 ( 3) SS BOND : angle 3.31742 ( 6) hydrogen bonds : bond 0.06874 ( 1374) hydrogen bonds : angle 4.44209 ( 2955) Misc. bond : bond 0.00335 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 584 time to evaluate : 0.872 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: C 55 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8197 (tt0) REVERT: C 93 LEU cc_start: 0.7904 (mp) cc_final: 0.7652 (tp) REVERT: C 106 LYS cc_start: 0.8091 (mttp) cc_final: 0.7433 (mmmt) REVERT: C 133 MET cc_start: 0.8711 (mmm) cc_final: 0.8420 (mtt) REVERT: D 10 ARG cc_start: 0.6697 (ptt-90) cc_final: 0.6229 (tpt170) REVERT: D 125 VAL cc_start: 0.9359 (t) cc_final: 0.9064 (m) REVERT: E 36 TYR cc_start: 0.7650 (p90) cc_final: 0.7418 (p90) REVERT: E 120 MET cc_start: 0.8831 (ptm) cc_final: 0.8553 (ptm) REVERT: E 125 SER cc_start: 0.7356 (m) cc_final: 0.6983 (p) REVERT: G 9 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8071 (tmtt) REVERT: G 52 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7389 (mt-10) REVERT: G 53 LYS cc_start: 0.7813 (mptt) cc_final: 0.7568 (pttm) REVERT: G 58 PRO cc_start: 0.7408 (Cg_endo) cc_final: 0.7172 (Cg_exo) REVERT: G 136 LYS cc_start: 0.8410 (ttmt) cc_final: 0.7952 (tttp) REVERT: G 140 ASP cc_start: 0.8031 (m-30) cc_final: 0.7787 (m-30) REVERT: H 115 ASP cc_start: 0.8194 (p0) cc_final: 0.7963 (p0) REVERT: I 61 ASN cc_start: 0.8200 (t0) cc_final: 0.7429 (t0) REVERT: I 115 ARG cc_start: 0.7391 (ttm170) cc_final: 0.7181 (tmt170) REVERT: J 11 LYS cc_start: 0.8351 (mttt) cc_final: 0.7871 (mttm) REVERT: J 56 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.7953 (p-80) REVERT: J 82 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7524 (tttt) REVERT: L 73 ASN cc_start: 0.7152 (m-40) cc_final: 0.6516 (m110) REVERT: L 77 HIS cc_start: 0.8009 (m-70) cc_final: 0.7752 (m90) REVERT: L 89 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7657 (p0) REVERT: L 107 VAL cc_start: 0.8633 (t) cc_final: 0.8410 (m) REVERT: M 15 MET cc_start: 0.8322 (tpt) cc_final: 0.8044 (mmm) REVERT: M 16 GLU cc_start: 0.7776 (tt0) cc_final: 0.7454 (tt0) REVERT: M 31 ASN cc_start: 0.8258 (m-40) cc_final: 0.7951 (m110) REVERT: M 32 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8374 (tm-30) REVERT: M 60 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7328 (mt) REVERT: M 75 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7427 (tp-100) REVERT: M 83 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6697 (tp30) REVERT: P 17 GLN cc_start: 0.8532 (mp10) cc_final: 0.7711 (mm-40) REVERT: P 44 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: R 49 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8462 (ttm110) REVERT: S 17 LYS cc_start: 0.7655 (tttt) cc_final: 0.7222 (tppt) REVERT: S 29 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5870 (pt0) outliers start: 68 outliers final: 36 residues processed: 624 average time/residue: 0.3209 time to fit residues: 310.0941 Evaluate side-chains 541 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 499 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 286 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS D 54 GLN D 66 GLN D 115 HIS E 111 GLN F 49 HIS F 74 ASN G 21 GLN G 129 ASN I 64 HIS K 49 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN O 51 HIS R 59 GLN R 60 HIS T 71 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099318 restraints weight = 85571.586| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.16 r_work: 0.2979 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 48857 Z= 0.294 Angle : 0.745 12.517 72790 Z= 0.376 Chirality : 0.042 0.320 9274 Planarity : 0.006 0.076 4082 Dihedral : 24.896 176.223 23942 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.00 % Favored : 92.00 % Rotamer: Outliers : 5.46 % Allowed : 16.32 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 1900 helix: 0.15 (0.18), residues: 746 sheet: -1.28 (0.27), residues: 335 loop : -2.11 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 87 TYR 0.018 0.002 TYR Q 49 PHE 0.023 0.002 PHE H 10 TRP 0.017 0.002 TRP C 18 HIS 0.011 0.002 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00577 (48853) covalent geometry : angle 0.74349 (72784) SS BOND : bond 0.01316 ( 3) SS BOND : angle 5.19944 ( 6) hydrogen bonds : bond 0.06994 ( 1374) hydrogen bonds : angle 4.28510 ( 2955) Misc. bond : bond 0.00174 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 521 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8263 (tt0) REVERT: C 93 LEU cc_start: 0.8073 (mp) cc_final: 0.7725 (tp) REVERT: C 106 LYS cc_start: 0.8278 (mttp) cc_final: 0.7620 (mmmt) REVERT: C 161 GLU cc_start: 0.8275 (tp30) cc_final: 0.7790 (pm20) REVERT: D 10 ARG cc_start: 0.7239 (ptt-90) cc_final: 0.6602 (tpt170) REVERT: D 125 VAL cc_start: 0.9434 (t) cc_final: 0.9136 (m) REVERT: E 111 GLN cc_start: 0.9281 (tt0) cc_final: 0.9042 (tt0) REVERT: G 48 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7499 (mm-30) REVERT: G 52 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7288 (mt-10) REVERT: G 106 ASN cc_start: 0.8786 (m110) cc_final: 0.8559 (m-40) REVERT: H 3 MET cc_start: 0.8474 (mmm) cc_final: 0.8146 (mmm) REVERT: H 115 ASP cc_start: 0.8436 (p0) cc_final: 0.8103 (p0) REVERT: I 58 TYR cc_start: 0.8197 (t80) cc_final: 0.7959 (t80) REVERT: I 61 ASN cc_start: 0.8604 (t0) cc_final: 0.7653 (t0) REVERT: I 65 GLN cc_start: 0.7377 (mt0) cc_final: 0.7100 (mp10) REVERT: I 115 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7075 (tmt170) REVERT: J 11 LYS cc_start: 0.8368 (mttt) cc_final: 0.7640 (mtpp) REVERT: J 45 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7491 (mt-10) REVERT: J 82 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7771 (tttt) REVERT: K 82 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8076 (mtmm) REVERT: L 77 HIS cc_start: 0.8291 (m-70) cc_final: 0.8083 (m90) REVERT: L 89 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7855 (p0) REVERT: M 15 MET cc_start: 0.8417 (tpt) cc_final: 0.8021 (mmm) REVERT: M 16 GLU cc_start: 0.7811 (tt0) cc_final: 0.7320 (tt0) REVERT: M 31 ASN cc_start: 0.8262 (m-40) cc_final: 0.7941 (m110) REVERT: M 32 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8438 (tm-30) REVERT: M 90 LEU cc_start: 0.9009 (mp) cc_final: 0.8805 (mp) REVERT: N 47 MET cc_start: 0.8493 (mmt) cc_final: 0.8163 (mmt) REVERT: N 52 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: P 17 GLN cc_start: 0.8927 (mp10) cc_final: 0.7554 (tp40) REVERT: P 34 ILE cc_start: 0.9338 (mt) cc_final: 0.9093 (mt) REVERT: P 44 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: P 50 GLN cc_start: 0.8235 (mt0) cc_final: 0.7897 (tm-30) REVERT: R 33 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8022 (mtmm) REVERT: R 48 ILE cc_start: 0.9492 (mt) cc_final: 0.9217 (mp) REVERT: S 16 LEU cc_start: 0.8615 (tp) cc_final: 0.7923 (pp) REVERT: S 17 LYS cc_start: 0.7779 (tttt) cc_final: 0.7297 (tppt) REVERT: T 45 ASP cc_start: 0.7880 (m-30) cc_final: 0.7673 (t0) REVERT: T 54 THR cc_start: 0.9135 (m) cc_final: 0.8627 (p) outliers start: 89 outliers final: 61 residues processed: 572 average time/residue: 0.3093 time to fit residues: 277.6810 Evaluate side-chains 553 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 488 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 104 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 21 GLN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS M 75 GLN M 101 GLN O 7 GLN R 60 HIS S 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097475 restraints weight = 86082.873| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.15 r_work: 0.2982 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 48857 Z= 0.359 Angle : 0.790 11.676 72790 Z= 0.396 Chirality : 0.044 0.340 9274 Planarity : 0.006 0.067 4082 Dihedral : 24.925 178.164 23939 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.53 % Favored : 91.58 % Rotamer: Outliers : 6.38 % Allowed : 18.28 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 1900 helix: 0.14 (0.18), residues: 750 sheet: -1.19 (0.27), residues: 341 loop : -2.20 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 49 TYR 0.021 0.002 TYR Q 49 PHE 0.022 0.002 PHE C 167 TRP 0.018 0.002 TRP C 18 HIS 0.009 0.002 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00701 (48853) covalent geometry : angle 0.78901 (72784) SS BOND : bond 0.00922 ( 3) SS BOND : angle 5.03893 ( 6) hydrogen bonds : bond 0.07165 ( 1374) hydrogen bonds : angle 4.34430 ( 2955) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 494 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8214 (tt0) REVERT: C 93 LEU cc_start: 0.8075 (mp) cc_final: 0.7780 (tp) REVERT: C 106 LYS cc_start: 0.8403 (mttp) cc_final: 0.7729 (mmmt) REVERT: C 161 GLU cc_start: 0.8218 (tp30) cc_final: 0.7657 (pm20) REVERT: D 10 ARG cc_start: 0.7464 (ptt-90) cc_final: 0.6712 (tpt170) REVERT: D 111 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: D 125 VAL cc_start: 0.9488 (t) cc_final: 0.9259 (m) REVERT: E 36 TYR cc_start: 0.8138 (p90) cc_final: 0.7546 (p90) REVERT: E 93 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7905 (mtt180) REVERT: E 111 GLN cc_start: 0.9270 (tt0) cc_final: 0.9020 (tt0) REVERT: E 153 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8143 (mt) REVERT: G 52 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7446 (mt-10) REVERT: G 104 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8701 (tt) REVERT: G 106 ASN cc_start: 0.8728 (m110) cc_final: 0.8482 (m-40) REVERT: H 38 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8406 (mm-30) REVERT: I 61 ASN cc_start: 0.8703 (t0) cc_final: 0.8044 (t0) REVERT: I 115 ARG cc_start: 0.7193 (ttm170) cc_final: 0.6895 (tmt170) REVERT: J 11 LYS cc_start: 0.8352 (mttt) cc_final: 0.7754 (mttm) REVERT: J 82 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7809 (tttt) REVERT: L 31 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8818 (ptt-90) REVERT: L 89 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7943 (p0) REVERT: M 15 MET cc_start: 0.8057 (tpt) cc_final: 0.7854 (mmm) REVERT: M 16 GLU cc_start: 0.7743 (tt0) cc_final: 0.7307 (tt0) REVERT: M 31 ASN cc_start: 0.8168 (m-40) cc_final: 0.7875 (m110) REVERT: M 32 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8398 (tm-30) REVERT: M 80 ARG cc_start: 0.7965 (ptt90) cc_final: 0.7522 (ppt170) REVERT: M 90 LEU cc_start: 0.8789 (mp) cc_final: 0.8585 (mp) REVERT: N 21 TYR cc_start: 0.8598 (p90) cc_final: 0.8261 (p90) REVERT: N 47 MET cc_start: 0.8610 (mmt) cc_final: 0.8216 (mmt) REVERT: N 52 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: P 17 GLN cc_start: 0.8894 (mp10) cc_final: 0.7414 (tp40) REVERT: P 34 ILE cc_start: 0.9296 (mt) cc_final: 0.9078 (mt) REVERT: P 44 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: P 50 GLN cc_start: 0.8205 (mt0) cc_final: 0.7896 (tm-30) REVERT: S 16 LEU cc_start: 0.8364 (tp) cc_final: 0.7715 (pp) REVERT: S 17 LYS cc_start: 0.7764 (tttt) cc_final: 0.7253 (tppt) REVERT: T 45 ASP cc_start: 0.7922 (m-30) cc_final: 0.7721 (t0) REVERT: T 54 THR cc_start: 0.9043 (m) cc_final: 0.8561 (p) outliers start: 104 outliers final: 80 residues processed: 553 average time/residue: 0.3146 time to fit residues: 273.1282 Evaluate side-chains 559 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 471 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 183 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 299 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS H 29 HIS I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098296 restraints weight = 85361.845| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.07 r_work: 0.3003 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 48857 Z= 0.308 Angle : 0.745 11.732 72790 Z= 0.374 Chirality : 0.042 0.321 9274 Planarity : 0.005 0.057 4082 Dihedral : 24.860 178.964 23936 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.58 % Favored : 91.58 % Rotamer: Outliers : 6.32 % Allowed : 20.80 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 1900 helix: 0.37 (0.19), residues: 740 sheet: -1.10 (0.27), residues: 347 loop : -2.27 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 32 TYR 0.019 0.002 TYR M 59 PHE 0.022 0.002 PHE C 167 TRP 0.018 0.002 TRP C 18 HIS 0.008 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00601 (48853) covalent geometry : angle 0.74341 (72784) SS BOND : bond 0.00825 ( 3) SS BOND : angle 4.78373 ( 6) hydrogen bonds : bond 0.06819 ( 1374) hydrogen bonds : angle 4.22441 ( 2955) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 494 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8076 (tt0) REVERT: C 93 LEU cc_start: 0.8087 (mp) cc_final: 0.7790 (tp) REVERT: C 106 LYS cc_start: 0.8428 (mttp) cc_final: 0.7787 (mmmt) REVERT: C 138 GLN cc_start: 0.8352 (tt0) cc_final: 0.7722 (pt0) REVERT: C 161 GLU cc_start: 0.7985 (tp30) cc_final: 0.7606 (pm20) REVERT: D 10 ARG cc_start: 0.7464 (ptt-90) cc_final: 0.6729 (tpt170) REVERT: D 111 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: D 125 VAL cc_start: 0.9464 (t) cc_final: 0.9234 (m) REVERT: E 36 TYR cc_start: 0.8106 (p90) cc_final: 0.7406 (p90) REVERT: E 93 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7613 (mtt180) REVERT: E 111 GLN cc_start: 0.9305 (tt0) cc_final: 0.9081 (tt0) REVERT: E 153 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8225 (mt) REVERT: F 71 ARG cc_start: 0.7125 (mmm160) cc_final: 0.6337 (ptm-80) REVERT: G 52 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7383 (mt-10) REVERT: G 104 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8602 (tt) REVERT: H 38 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8315 (mm-30) REVERT: I 61 ASN cc_start: 0.8742 (t0) cc_final: 0.7771 (m-40) REVERT: I 115 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6834 (tmt170) REVERT: J 11 LYS cc_start: 0.8281 (mttt) cc_final: 0.7747 (mttm) REVERT: J 82 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7797 (tttt) REVERT: K 81 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7261 (mtm-85) REVERT: L 31 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8723 (ptt-90) REVERT: L 89 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7871 (p0) REVERT: M 15 MET cc_start: 0.8081 (tpt) cc_final: 0.7743 (mmm) REVERT: M 16 GLU cc_start: 0.7758 (tt0) cc_final: 0.7341 (tt0) REVERT: M 19 LEU cc_start: 0.9224 (mm) cc_final: 0.8997 (mm) REVERT: M 31 ASN cc_start: 0.8365 (m-40) cc_final: 0.8064 (m110) REVERT: M 32 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8411 (tm-30) REVERT: N 21 TYR cc_start: 0.8580 (p90) cc_final: 0.8206 (p90) REVERT: N 47 MET cc_start: 0.8619 (mmt) cc_final: 0.8238 (mmt) REVERT: O 74 ASP cc_start: 0.7150 (t70) cc_final: 0.6110 (t0) REVERT: P 17 GLN cc_start: 0.8841 (mp10) cc_final: 0.7372 (tp40) REVERT: P 44 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: P 50 GLN cc_start: 0.8174 (mt0) cc_final: 0.7888 (tm-30) REVERT: S 16 LEU cc_start: 0.8257 (tp) cc_final: 0.7596 (pp) REVERT: S 17 LYS cc_start: 0.7707 (tttt) cc_final: 0.7154 (tppt) REVERT: T 54 THR cc_start: 0.9015 (m) cc_final: 0.8544 (p) outliers start: 103 outliers final: 79 residues processed: 551 average time/residue: 0.3132 time to fit residues: 270.5917 Evaluate side-chains 561 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 475 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 310 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN I 57 ASN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098371 restraints weight = 85332.712| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.07 r_work: 0.3005 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 48857 Z= 0.296 Angle : 0.734 12.438 72790 Z= 0.369 Chirality : 0.041 0.320 9274 Planarity : 0.005 0.055 4082 Dihedral : 24.825 178.711 23936 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.05 % Favored : 91.11 % Rotamer: Outliers : 6.87 % Allowed : 21.23 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1900 helix: 0.42 (0.19), residues: 745 sheet: -1.08 (0.27), residues: 349 loop : -2.30 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 45 TYR 0.019 0.002 TYR M 59 PHE 0.019 0.002 PHE C 167 TRP 0.017 0.002 TRP C 18 HIS 0.008 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00577 (48853) covalent geometry : angle 0.73310 (72784) SS BOND : bond 0.00951 ( 3) SS BOND : angle 4.34793 ( 6) hydrogen bonds : bond 0.06757 ( 1374) hydrogen bonds : angle 4.18261 ( 2955) Misc. bond : bond 0.00211 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 497 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7987 (tt0) REVERT: C 93 LEU cc_start: 0.8006 (mp) cc_final: 0.7754 (tp) REVERT: C 106 LYS cc_start: 0.8399 (mttp) cc_final: 0.7773 (mmmt) REVERT: C 138 GLN cc_start: 0.8392 (tt0) cc_final: 0.7792 (pt0) REVERT: C 161 GLU cc_start: 0.7966 (tp30) cc_final: 0.7574 (pm20) REVERT: D 10 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.6767 (tpt170) REVERT: D 111 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: D 125 VAL cc_start: 0.9468 (t) cc_final: 0.9219 (m) REVERT: D 126 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7427 (p0) REVERT: E 45 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7723 (ttt-90) REVERT: E 111 GLN cc_start: 0.9293 (tt0) cc_final: 0.9082 (tt0) REVERT: E 142 CYS cc_start: 0.8343 (m) cc_final: 0.8001 (m) REVERT: E 153 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8238 (mt) REVERT: F 54 TYR cc_start: 0.7375 (m-80) cc_final: 0.6929 (m-80) REVERT: F 71 ARG cc_start: 0.6851 (mmm160) cc_final: 0.6370 (ptm-80) REVERT: G 52 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7246 (mt-10) REVERT: G 104 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8705 (tt) REVERT: H 38 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8258 (mm-30) REVERT: I 61 ASN cc_start: 0.8537 (t0) cc_final: 0.7921 (m-40) REVERT: I 66 GLN cc_start: 0.8097 (pt0) cc_final: 0.7876 (pp30) REVERT: J 11 LYS cc_start: 0.8297 (mttt) cc_final: 0.7768 (mttm) REVERT: J 82 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7743 (tttt) REVERT: K 45 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6990 (p0) REVERT: L 31 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8640 (ptt-90) REVERT: L 89 ASP cc_start: 0.8344 (m-30) cc_final: 0.7977 (p0) REVERT: M 15 MET cc_start: 0.8123 (tpt) cc_final: 0.7842 (mmm) REVERT: M 16 GLU cc_start: 0.7721 (tt0) cc_final: 0.7299 (tt0) REVERT: M 31 ASN cc_start: 0.8342 (m-40) cc_final: 0.8029 (m110) REVERT: M 32 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8437 (tm-30) REVERT: M 42 ASN cc_start: 0.8189 (m-40) cc_final: 0.7520 (t0) REVERT: M 90 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8710 (mp) REVERT: N 21 TYR cc_start: 0.8559 (p90) cc_final: 0.8258 (p90) REVERT: N 47 MET cc_start: 0.8586 (mmt) cc_final: 0.8274 (mmt) REVERT: N 52 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8564 (mm-30) REVERT: P 17 GLN cc_start: 0.8831 (mp10) cc_final: 0.7381 (tp40) REVERT: P 44 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: P 50 GLN cc_start: 0.8185 (mt0) cc_final: 0.7905 (tm-30) REVERT: P 73 LEU cc_start: 0.9329 (mt) cc_final: 0.9112 (mp) REVERT: R 41 TYR cc_start: 0.8610 (m-80) cc_final: 0.8078 (m-80) REVERT: R 49 ARG cc_start: 0.9057 (ttm110) cc_final: 0.7850 (mtm-85) REVERT: S 16 LEU cc_start: 0.8139 (tp) cc_final: 0.7465 (pp) REVERT: S 17 LYS cc_start: 0.7666 (tttt) cc_final: 0.7125 (tppt) REVERT: S 25 LYS cc_start: 0.7268 (mmmt) cc_final: 0.7058 (mptt) REVERT: S 47 HIS cc_start: 0.8242 (t70) cc_final: 0.7612 (m-70) REVERT: T 54 THR cc_start: 0.9002 (m) cc_final: 0.8563 (p) outliers start: 112 outliers final: 84 residues processed: 562 average time/residue: 0.3040 time to fit residues: 267.7367 Evaluate side-chains 573 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 480 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 106 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 263 optimal weight: 0.4980 chunk 281 optimal weight: 0.8980 chunk 236 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN I 57 ASN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098434 restraints weight = 85184.441| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.06 r_work: 0.3006 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 48857 Z= 0.293 Angle : 0.729 12.746 72790 Z= 0.367 Chirality : 0.041 0.318 9274 Planarity : 0.005 0.052 4082 Dihedral : 24.785 178.122 23934 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.32 % Favored : 90.95 % Rotamer: Outliers : 7.61 % Allowed : 20.74 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 1900 helix: 0.44 (0.19), residues: 741 sheet: -1.19 (0.26), residues: 348 loop : -2.33 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 94 TYR 0.018 0.002 TYR Q 49 PHE 0.020 0.002 PHE C 167 TRP 0.017 0.002 TRP C 18 HIS 0.007 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00571 (48853) covalent geometry : angle 0.72807 (72784) SS BOND : bond 0.00875 ( 3) SS BOND : angle 4.35107 ( 6) hydrogen bonds : bond 0.06760 ( 1374) hydrogen bonds : angle 4.19272 ( 2955) Misc. bond : bond 0.00189 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 488 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7977 (tt0) REVERT: C 93 LEU cc_start: 0.7955 (mp) cc_final: 0.7590 (tp) REVERT: C 106 LYS cc_start: 0.8384 (mttp) cc_final: 0.7744 (mmmt) REVERT: C 161 GLU cc_start: 0.7993 (tp30) cc_final: 0.7554 (pm20) REVERT: D 10 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.6794 (tpt170) REVERT: D 111 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: D 125 VAL cc_start: 0.9467 (t) cc_final: 0.9220 (m) REVERT: D 126 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7380 (p0) REVERT: E 111 GLN cc_start: 0.9308 (tt0) cc_final: 0.9099 (tt0) REVERT: E 142 CYS cc_start: 0.8364 (m) cc_final: 0.8008 (m) REVERT: E 153 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8150 (mt) REVERT: F 54 TYR cc_start: 0.7362 (m-80) cc_final: 0.6824 (m-80) REVERT: F 71 ARG cc_start: 0.6908 (mmm160) cc_final: 0.6495 (ptm-80) REVERT: G 52 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6871 (mt-10) REVERT: G 104 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8592 (tt) REVERT: H 38 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8441 (mm-30) REVERT: I 61 ASN cc_start: 0.8579 (t0) cc_final: 0.8021 (m-40) REVERT: I 66 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7819 (pp30) REVERT: J 11 LYS cc_start: 0.8270 (mttt) cc_final: 0.7781 (mttm) REVERT: K 45 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6996 (p0) REVERT: L 31 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8620 (ptt-90) REVERT: L 89 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8039 (p0) REVERT: M 16 GLU cc_start: 0.7845 (tt0) cc_final: 0.7365 (tt0) REVERT: M 31 ASN cc_start: 0.8330 (m-40) cc_final: 0.7972 (m110) REVERT: M 32 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8435 (tm-30) REVERT: M 42 ASN cc_start: 0.8211 (m-40) cc_final: 0.7534 (t0) REVERT: M 80 ARG cc_start: 0.8025 (ptt90) cc_final: 0.7576 (ppt170) REVERT: M 90 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8728 (mp) REVERT: N 21 TYR cc_start: 0.8575 (p90) cc_final: 0.8252 (p90) REVERT: N 47 MET cc_start: 0.8587 (mmp) cc_final: 0.8300 (mmt) REVERT: N 52 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8532 (mm-30) REVERT: O 74 ASP cc_start: 0.7022 (t70) cc_final: 0.6222 (t0) REVERT: P 17 GLN cc_start: 0.8846 (mp10) cc_final: 0.7411 (tp40) REVERT: P 44 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: P 50 GLN cc_start: 0.8194 (mt0) cc_final: 0.7907 (tm-30) REVERT: P 73 LEU cc_start: 0.9313 (mt) cc_final: 0.9100 (mp) REVERT: S 16 LEU cc_start: 0.8163 (tp) cc_final: 0.7504 (pp) REVERT: S 17 LYS cc_start: 0.7680 (tttt) cc_final: 0.7092 (tppt) REVERT: S 25 LYS cc_start: 0.7368 (mmmt) cc_final: 0.7153 (mptt) REVERT: S 47 HIS cc_start: 0.7974 (t70) cc_final: 0.7071 (m-70) REVERT: T 54 THR cc_start: 0.8996 (m) cc_final: 0.8556 (p) outliers start: 124 outliers final: 98 residues processed: 557 average time/residue: 0.3040 time to fit residues: 265.7500 Evaluate side-chains 589 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 481 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN I 57 ASN K 47 GLN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097503 restraints weight = 85837.468| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.11 r_work: 0.2989 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 48857 Z= 0.318 Angle : 0.757 12.685 72790 Z= 0.380 Chirality : 0.042 0.328 9274 Planarity : 0.005 0.052 4082 Dihedral : 24.804 179.781 23934 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.58 % Favored : 90.68 % Rotamer: Outliers : 7.61 % Allowed : 21.47 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 1900 helix: 0.38 (0.19), residues: 740 sheet: -1.19 (0.27), residues: 358 loop : -2.31 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 94 TYR 0.019 0.002 TYR Q 9 PHE 0.021 0.002 PHE C 167 TRP 0.018 0.002 TRP C 18 HIS 0.008 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00621 (48853) covalent geometry : angle 0.75566 (72784) SS BOND : bond 0.00703 ( 3) SS BOND : angle 4.57561 ( 6) hydrogen bonds : bond 0.07020 ( 1374) hydrogen bonds : angle 4.22549 ( 2955) Misc. bond : bond 0.00178 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 497 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8739 (t-90) REVERT: C 18 TRP cc_start: 0.8611 (m-90) cc_final: 0.8323 (m-90) REVERT: C 55 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7978 (tt0) REVERT: C 93 LEU cc_start: 0.7963 (mp) cc_final: 0.7607 (tp) REVERT: C 106 LYS cc_start: 0.8389 (mttp) cc_final: 0.7691 (mmmt) REVERT: C 161 GLU cc_start: 0.8079 (tp30) cc_final: 0.7543 (pm20) REVERT: D 10 ARG cc_start: 0.7647 (ptt-90) cc_final: 0.6811 (tpt170) REVERT: D 111 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: D 125 VAL cc_start: 0.9473 (t) cc_final: 0.9222 (m) REVERT: D 126 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7340 (p0) REVERT: E 111 GLN cc_start: 0.9335 (tt0) cc_final: 0.9129 (tt0) REVERT: E 142 CYS cc_start: 0.8402 (m) cc_final: 0.8049 (m) REVERT: E 153 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8170 (mt) REVERT: F 40 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7446 (mtm180) REVERT: F 54 TYR cc_start: 0.7303 (m-80) cc_final: 0.6954 (m-80) REVERT: F 71 ARG cc_start: 0.7015 (mmm160) cc_final: 0.6359 (ptm-80) REVERT: G 52 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7042 (mt-10) REVERT: G 104 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8733 (tt) REVERT: H 38 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8450 (mm-30) REVERT: I 47 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.4994 (pm20) REVERT: I 61 ASN cc_start: 0.8608 (t0) cc_final: 0.7989 (m-40) REVERT: I 66 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: I 87 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7876 (mt) REVERT: J 11 LYS cc_start: 0.8326 (mttt) cc_final: 0.7761 (mttm) REVERT: K 24 ASN cc_start: 0.5145 (t0) cc_final: 0.4625 (t0) REVERT: K 45 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6650 (p0) REVERT: L 31 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8622 (ptt-90) REVERT: L 89 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8051 (p0) REVERT: M 16 GLU cc_start: 0.7875 (tt0) cc_final: 0.7398 (tt0) REVERT: M 31 ASN cc_start: 0.8378 (m-40) cc_final: 0.8022 (m110) REVERT: M 42 ASN cc_start: 0.8233 (m-40) cc_final: 0.7462 (t0) REVERT: M 80 ARG cc_start: 0.8090 (ptt90) cc_final: 0.7615 (ppt170) REVERT: M 90 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8708 (mp) REVERT: N 21 TYR cc_start: 0.8619 (p90) cc_final: 0.8339 (p90) REVERT: N 47 MET cc_start: 0.8716 (mmp) cc_final: 0.8388 (mmt) REVERT: N 52 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8510 (mm-30) REVERT: O 74 ASP cc_start: 0.7243 (t70) cc_final: 0.6049 (t0) REVERT: P 17 GLN cc_start: 0.8933 (mp10) cc_final: 0.7473 (tp40) REVERT: P 44 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: R 32 TYR cc_start: 0.8717 (p90) cc_final: 0.8423 (p90) REVERT: R 47 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8885 (mtmt) REVERT: R 49 ARG cc_start: 0.9092 (ttm110) cc_final: 0.8330 (mtm110) REVERT: S 16 LEU cc_start: 0.8201 (tp) cc_final: 0.7529 (pp) REVERT: S 17 LYS cc_start: 0.7643 (tttt) cc_final: 0.7116 (tppt) REVERT: S 25 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7263 (mptt) REVERT: S 47 HIS cc_start: 0.7993 (t70) cc_final: 0.7110 (m-70) REVERT: T 54 THR cc_start: 0.9009 (m) cc_final: 0.8559 (p) REVERT: U 12 MET cc_start: 0.8449 (mmm) cc_final: 0.7772 (mmt) outliers start: 124 outliers final: 97 residues processed: 566 average time/residue: 0.2936 time to fit residues: 262.1556 Evaluate side-chains 597 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 487 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 80 TRP Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 293 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN I 64 HIS I 146 GLN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN Q 65 ASN R 59 GLN R 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101425 restraints weight = 84736.647| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.06 r_work: 0.3050 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 48857 Z= 0.181 Angle : 0.650 12.378 72790 Z= 0.329 Chirality : 0.037 0.275 9274 Planarity : 0.005 0.056 4082 Dihedral : 24.644 179.828 23934 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.00 % Favored : 91.21 % Rotamer: Outliers : 6.26 % Allowed : 23.37 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1900 helix: 0.75 (0.19), residues: 744 sheet: -1.17 (0.27), residues: 347 loop : -2.20 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 81 TYR 0.022 0.002 TYR Q 9 PHE 0.019 0.002 PHE C 167 TRP 0.020 0.001 TRP C 18 HIS 0.006 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00352 (48853) covalent geometry : angle 0.64889 (72784) SS BOND : bond 0.00786 ( 3) SS BOND : angle 4.17898 ( 6) hydrogen bonds : bond 0.05995 ( 1374) hydrogen bonds : angle 3.96184 ( 2955) Misc. bond : bond 0.00215 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 493 time to evaluate : 0.791 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: C 18 TRP cc_start: 0.8359 (m-90) cc_final: 0.8148 (m-90) REVERT: C 55 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8018 (tt0) REVERT: C 93 LEU cc_start: 0.8018 (mp) cc_final: 0.7680 (tp) REVERT: C 106 LYS cc_start: 0.8339 (mttp) cc_final: 0.7706 (mmmt) REVERT: C 138 GLN cc_start: 0.8418 (tt0) cc_final: 0.7727 (pt0) REVERT: C 161 GLU cc_start: 0.8144 (tp30) cc_final: 0.7550 (pm20) REVERT: D 10 ARG cc_start: 0.7466 (ptt-90) cc_final: 0.6705 (tpt170) REVERT: D 125 VAL cc_start: 0.9414 (t) cc_final: 0.9078 (m) REVERT: E 142 CYS cc_start: 0.8467 (m) cc_final: 0.8109 (m) REVERT: F 40 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7384 (mtm180) REVERT: F 54 TYR cc_start: 0.7194 (m-80) cc_final: 0.6864 (m-80) REVERT: G 52 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6926 (mt-10) REVERT: G 104 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8559 (tt) REVERT: I 61 ASN cc_start: 0.8604 (t0) cc_final: 0.7948 (m-40) REVERT: I 66 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (pp30) REVERT: I 115 ARG cc_start: 0.7036 (ttm170) cc_final: 0.6699 (tmt170) REVERT: J 10 LEU cc_start: 0.9002 (mp) cc_final: 0.8726 (mm) REVERT: J 11 LYS cc_start: 0.8432 (mttt) cc_final: 0.7838 (mttm) REVERT: K 24 ASN cc_start: 0.5228 (t0) cc_final: 0.4861 (t0) REVERT: K 45 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.6991 (p0) REVERT: L 31 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8483 (ptt-90) REVERT: L 70 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6757 (mm-30) REVERT: L 89 ASP cc_start: 0.8209 (m-30) cc_final: 0.7880 (p0) REVERT: M 16 GLU cc_start: 0.7847 (tt0) cc_final: 0.7318 (tt0) REVERT: M 31 ASN cc_start: 0.8345 (m-40) cc_final: 0.7922 (m-40) REVERT: M 32 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8324 (tm-30) REVERT: M 90 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (mp) REVERT: N 21 TYR cc_start: 0.8565 (p90) cc_final: 0.8327 (p90) REVERT: N 47 MET cc_start: 0.8526 (mmp) cc_final: 0.8310 (mmt) REVERT: N 52 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8477 (mm-30) REVERT: O 39 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8699 (mp) REVERT: O 74 ASP cc_start: 0.7112 (t70) cc_final: 0.5924 (t0) REVERT: P 17 GLN cc_start: 0.8919 (mp10) cc_final: 0.7513 (tp40) REVERT: R 47 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8726 (mtmt) REVERT: R 49 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8297 (mtm110) REVERT: S 16 LEU cc_start: 0.8182 (tp) cc_final: 0.7475 (pp) REVERT: S 17 LYS cc_start: 0.7475 (tttt) cc_final: 0.6984 (tppt) REVERT: S 25 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7243 (mptt) REVERT: S 47 HIS cc_start: 0.7963 (t70) cc_final: 0.7181 (m-70) REVERT: T 54 THR cc_start: 0.8948 (m) cc_final: 0.8536 (p) REVERT: U 12 MET cc_start: 0.8010 (mmm) cc_final: 0.7548 (mmt) outliers start: 102 outliers final: 83 residues processed: 548 average time/residue: 0.2814 time to fit residues: 241.8859 Evaluate side-chains 573 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 484 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 58 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 242 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 217 optimal weight: 0.0070 chunk 212 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 overall best weight: 1.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 HIS O 37 GLN O 42 HIS P 50 GLN Q 65 ASN R 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101390 restraints weight = 85034.467| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.06 r_work: 0.3050 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 48857 Z= 0.186 Angle : 0.649 13.121 72790 Z= 0.327 Chirality : 0.036 0.284 9274 Planarity : 0.005 0.056 4082 Dihedral : 24.598 178.996 23934 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.11 % Favored : 91.26 % Rotamer: Outliers : 5.58 % Allowed : 23.99 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1900 helix: 0.83 (0.19), residues: 745 sheet: -1.07 (0.27), residues: 354 loop : -2.21 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 65 TYR 0.028 0.002 TYR O 69 PHE 0.019 0.002 PHE C 167 TRP 0.017 0.001 TRP C 18 HIS 0.006 0.001 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00364 (48853) covalent geometry : angle 0.64781 (72784) SS BOND : bond 0.00556 ( 3) SS BOND : angle 4.05470 ( 6) hydrogen bonds : bond 0.05905 ( 1374) hydrogen bonds : angle 3.96039 ( 2955) Misc. bond : bond 0.00213 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 483 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 LEU cc_start: 0.8017 (mp) cc_final: 0.7684 (tp) REVERT: C 106 LYS cc_start: 0.8343 (mttp) cc_final: 0.7680 (mmmt) REVERT: C 109 GLU cc_start: 0.6033 (pt0) cc_final: 0.5730 (pt0) REVERT: C 138 GLN cc_start: 0.8424 (tt0) cc_final: 0.7704 (pt0) REVERT: C 161 GLU cc_start: 0.8131 (tp30) cc_final: 0.7583 (pm20) REVERT: D 10 ARG cc_start: 0.7452 (ptt-90) cc_final: 0.6697 (tpt170) REVERT: D 104 ARG cc_start: 0.6677 (ptm160) cc_final: 0.6265 (ttp80) REVERT: D 110 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8080 (mmt90) REVERT: D 111 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: D 125 VAL cc_start: 0.9425 (t) cc_final: 0.9070 (m) REVERT: E 142 CYS cc_start: 0.8456 (m) cc_final: 0.8098 (m) REVERT: F 40 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7330 (mtm180) REVERT: F 54 TYR cc_start: 0.7127 (m-80) cc_final: 0.6904 (m-80) REVERT: F 71 ARG cc_start: 0.6847 (mmm160) cc_final: 0.6277 (ptm-80) REVERT: G 52 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6926 (mt-10) REVERT: G 104 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8628 (tt) REVERT: I 47 GLN cc_start: 0.5545 (OUTLIER) cc_final: 0.4975 (pm20) REVERT: I 61 ASN cc_start: 0.8559 (t0) cc_final: 0.7972 (m-40) REVERT: I 66 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (pp30) REVERT: I 115 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6693 (tmt170) REVERT: J 10 LEU cc_start: 0.9025 (mp) cc_final: 0.8770 (mm) REVERT: J 11 LYS cc_start: 0.8414 (mttt) cc_final: 0.7831 (mttm) REVERT: K 45 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.6974 (p0) REVERT: L 70 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6848 (mm-30) REVERT: L 89 ASP cc_start: 0.8183 (m-30) cc_final: 0.7870 (p0) REVERT: M 16 GLU cc_start: 0.7815 (tt0) cc_final: 0.7247 (tt0) REVERT: M 31 ASN cc_start: 0.8349 (m-40) cc_final: 0.7859 (m-40) REVERT: M 32 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8307 (tm-30) REVERT: N 52 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8457 (mm-30) REVERT: O 39 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8936 (mp) REVERT: O 74 ASP cc_start: 0.7117 (t70) cc_final: 0.5920 (t0) REVERT: P 17 GLN cc_start: 0.8932 (mp10) cc_final: 0.7530 (tp40) REVERT: P 44 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: P 90 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: R 47 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8758 (mtmt) REVERT: R 49 ARG cc_start: 0.9104 (ttm110) cc_final: 0.8785 (mtm-85) REVERT: S 16 LEU cc_start: 0.8175 (tp) cc_final: 0.7483 (pp) REVERT: S 17 LYS cc_start: 0.7478 (tttt) cc_final: 0.6967 (tppt) REVERT: S 25 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7144 (mptt) REVERT: S 47 HIS cc_start: 0.7984 (t70) cc_final: 0.7184 (m-70) REVERT: T 54 THR cc_start: 0.8951 (m) cc_final: 0.8532 (p) REVERT: U 12 MET cc_start: 0.8182 (mmm) cc_final: 0.7676 (mmt) outliers start: 91 outliers final: 76 residues processed: 535 average time/residue: 0.2710 time to fit residues: 228.7762 Evaluate side-chains 546 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 461 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 80 TRP Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 188 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 159 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN H 93 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 HIS O 37 GLN P 50 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN R 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101153 restraints weight = 85219.443| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.07 r_work: 0.3044 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48857 Z= 0.202 Angle : 0.658 13.308 72790 Z= 0.331 Chirality : 0.037 0.288 9274 Planarity : 0.005 0.056 4082 Dihedral : 24.580 178.678 23934 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.16 % Favored : 91.26 % Rotamer: Outliers : 5.64 % Allowed : 24.36 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1900 helix: 0.79 (0.19), residues: 740 sheet: -1.16 (0.27), residues: 361 loop : -2.19 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 112 TYR 0.025 0.002 TYR O 69 PHE 0.019 0.002 PHE C 167 TRP 0.011 0.001 TRP P 80 HIS 0.005 0.001 HIS O 18 Details of bonding type rmsd covalent geometry : bond 0.00394 (48853) covalent geometry : angle 0.65678 (72784) SS BOND : bond 0.00578 ( 3) SS BOND : angle 4.49402 ( 6) hydrogen bonds : bond 0.05964 ( 1374) hydrogen bonds : angle 3.96101 ( 2955) Misc. bond : bond 0.00204 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11355.48 seconds wall clock time: 194 minutes 40.95 seconds (11680.95 seconds total)