Starting phenix.real_space_refine on Tue Sep 15 19:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xyu_6790/09_2026/5xyu_6790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xyu_6790/09_2026/5xyu_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_6790/09_2026/5xyu_6790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xyu_6790/09_2026/5xyu_6790_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xyu_6790/09_2026/5xyu_6790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xyu_6790/09_2026/5xyu_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-2.2.1-6174/lib/python3.11/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: 8.87, 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: 3.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.71 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: 20.48 Time building geometry restraints manager: 4.27 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=" C LEU N 53 " pdb=" N PRO N 54 " ideal model delta sigma weight residual 1.332 1.387 -0.056 1.30e-02 5.92e+03 1.82e+01 ... (remaining 48848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 71996 3.03 - 6.06: 712 6.06 - 9.09: 48 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=" 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 angle pdb=" N ARG L 114 " pdb=" CA ARG L 114 " pdb=" C ARG L 114 " ideal model delta sigma weight residual 111.28 119.26 -7.98 1.09e+00 8.42e-01 5.36e+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: 8558 0.127 - 0.253: 677 0.253 - 0.380: 24 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: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 51.980 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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= 0.526 Angle : 0.951 58.518 72790 Z= 0.673 Chirality : 0.072 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/Z covalent geometry : bond 0.00637 / 0.46 (48853) covalent geometry : angle 0.90890 / 0.66 (72784) SS BOND : bond 0.48568 / 46.53 ( 3) SS BOND : angle 30.84923 / 36.71 ( 6) hydrogen bonds : bond 0.28555 / 30.78 ( 1374) hydrogen bonds : angle 9.41847 / 12.02 ( 2955) Misc. bond : bond 0.34695 / 17.35 ( 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 : 0.837 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: 0.8338 (t) cc_final: 0.8077 (m) REVERT: C 55 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6809 (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: 0.8069 (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: 0.7824 (mt-10) REVERT: D 10 ARG cc_start: 0.7517 (ptt-90) cc_final: 0.6284 (tpt170) REVERT: D 17 VAL cc_start: 0.7872 (m) cc_final: 0.7660 (p) REVERT: D 48 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6891 (pm20) REVERT: D 65 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8240 (ttmm) REVERT: D 91 SER cc_start: 0.8900 (m) cc_final: 0.8630 (p) REVERT: D 99 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6819 (tpt170) REVERT: D 102 LEU cc_start: 0.7914 (tt) cc_final: 0.7709 (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: 0.8746 (m) REVERT: D 174 ARG cc_start: 0.6651 (ptm160) cc_final: 0.6350 (mmt-90) REVERT: D 177 VAL cc_start: 0.9003 (t) cc_final: 0.8725 (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: 0.7209 (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: 0.7318 (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: 0.7296 (mmt-90) cc_final: 0.6741 (mmt180) REVERT: G 58 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.6781 (Cg_exo) REVERT: G 71 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8357 (Cg_exo) REVERT: G 126 ASP cc_start: 0.7951 (m-30) cc_final: 0.7568 (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: 0.7274 (m-30) REVERT: H 3 MET cc_start: 0.8307 (mmm) cc_final: 0.7700 (mmm) REVERT: H 31 LYS cc_start: 0.8906 (tptm) cc_final: 0.8581 (ttpt) REVERT: H 38 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8135 (mm-30) REVERT: H 78 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7507 (ptm-80) REVERT: H 115 ASP cc_start: 0.8710 (p0) cc_final: 0.7962 (p0) REVERT: I 33 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7669 (ttmt) REVERT: I 61 ASN cc_start: 0.8331 (t0) cc_final: 0.8072 (t0) REVERT: I 107 LEU cc_start: 0.7159 (mt) cc_final: 0.6823 (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: 0.7064 (mtpp) REVERT: J 45 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7465 (mt-10) REVERT: J 46 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7733 (ttpp) REVERT: J 47 ASN cc_start: 0.8049 (m-40) cc_final: 0.7709 (m-40) REVERT: J 53 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6855 (mtt180) REVERT: J 71 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7534 (mttm) REVERT: K 32 ILE cc_start: 0.8511 (mp) cc_final: 0.8271 (pt) REVERT: K 41 VAL cc_start: 0.8287 (t) cc_final: 0.7994 (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: 0.8394 (p) REVERT: L 102 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6779 (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: 0.8203 (m) REVERT: M 16 GLU cc_start: 0.7300 (tt0) cc_final: 0.7068 (tt0) REVERT: M 65 LYS cc_start: 0.7333 (mptt) cc_final: 0.6771 (mmmt) REVERT: M 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7153 (tp30) REVERT: N 4 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7005 (mtpt) REVERT: N 26 LYS cc_start: 0.7673 (tttp) cc_final: 0.7454 (tttm) REVERT: O 44 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8411 (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: 0.6600 (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: 0.8157 (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: 0.8134 (mp) REVERT: R 66 VAL cc_start: 0.8709 (t) cc_final: 0.8381 (p) REVERT: S 33 THR cc_start: 0.7922 (m) cc_final: 0.7624 (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: 0.3342 time to fit residues: 337.3766 Evaluate side-chains 513 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 498 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 HIS C 68 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS G 25 GLN H 63 GLN H 93 ASN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 75 GLN O 7 GLN O 37 GLN Q 62 HIS Q 65 ASN R 59 GLN R 60 HIS S 29 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105193 restraints weight = 84579.970| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.05 r_work: 0.3109 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 48857 Z= 0.165 Angle : 0.693 13.292 72790 Z= 0.397 Chirality : 0.047 0.594 9274 Planarity : 0.006 0.064 4082 Dihedral : 24.923 178.387 23958 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 1.42 % Allowed : 5.47 % Favored : 93.11 % Rotamer: Outliers : 3.56 % Allowed : 13.37 % Favored : 83.07 % 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: -2.49 (0.16), residues: 1900 helix: -0.79 (0.17), residues: 741 sheet: -1.84 (0.24), residues: 335 loop : -2.31 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 80 TYR 0.016 0.002 TYR J 13 PHE 0.014 0.002 PHE H 10 TRP 0.019 0.002 TRP C 18 HIS 0.014 0.002 HIS S 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (48853) covalent geometry : angle 0.69108 / 0.40 (72784) SS BOND : bond 0.01390 / 0.86 ( 3) SS BOND : angle 5.02929 / 6.69 ( 6) hydrogen bonds : bond 0.10147 / 10.90 ( 1374) hydrogen bonds : angle 4.95024 / 6.50 ( 2955) Misc. bond : bond 0.02772 / 1.39 ( 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 621 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 563 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 THR cc_start: 0.6923 (t) cc_final: 0.6660 (t) REVERT: C 55 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8083 (tt0) REVERT: C 93 LEU cc_start: 0.7910 (mp) cc_final: 0.7656 (tp) REVERT: C 106 LYS cc_start: 0.8035 (mttp) cc_final: 0.7353 (mmmt) REVERT: D 10 ARG cc_start: 0.7013 (ptt-90) cc_final: 0.6355 (tpt170) REVERT: D 104 ARG cc_start: 0.7012 (ttm-80) cc_final: 0.6775 (ptm160) REVERT: D 125 VAL cc_start: 0.9363 (t) cc_final: 0.9094 (m) REVERT: E 36 TYR cc_start: 0.7463 (p90) cc_final: 0.7215 (p90) REVERT: E 125 SER cc_start: 0.7397 (m) cc_final: 0.7068 (p) REVERT: G 52 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7559 (mt-10) REVERT: G 58 PRO cc_start: 0.7548 (Cg_endo) cc_final: 0.7321 (Cg_exo) REVERT: G 140 ASP cc_start: 0.8060 (m-30) cc_final: 0.7808 (m-30) REVERT: G 146 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7816 (mm-30) REVERT: H 51 THR cc_start: 0.7970 (m) cc_final: 0.7768 (m) REVERT: I 61 ASN cc_start: 0.8241 (t0) cc_final: 0.7578 (t0) REVERT: I 115 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7262 (tmt170) REVERT: J 11 LYS cc_start: 0.8293 (mttt) cc_final: 0.7706 (mtpp) REVERT: J 71 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7875 (mttm) REVERT: J 82 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7564 (tttt) REVERT: L 6 GLN cc_start: 0.8937 (tt0) cc_final: 0.8726 (tt0) REVERT: L 73 ASN cc_start: 0.6998 (m-40) cc_final: 0.6289 (m-40) REVERT: L 89 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7498 (p0) REVERT: M 16 GLU cc_start: 0.7806 (tt0) cc_final: 0.7464 (tt0) REVERT: M 31 ASN cc_start: 0.8387 (m-40) cc_final: 0.8180 (m110) REVERT: M 32 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8472 (tm-30) REVERT: P 17 GLN cc_start: 0.8571 (mp10) cc_final: 0.7702 (mm-40) REVERT: P 44 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: P 50 GLN cc_start: 0.8093 (mt0) cc_final: 0.7853 (tm-30) REVERT: Q 54 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8602 (ttp80) REVERT: S 17 LYS cc_start: 0.7844 (tttt) cc_final: 0.7471 (tppt) REVERT: T 83 LEU cc_start: 0.8744 (tp) cc_final: 0.8543 (tt) REVERT: U 4 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8567 (t) outliers start: 58 outliers final: 33 residues processed: 596 average time/residue: 0.3153 time to fit residues: 294.1831 Evaluate side-chains 545 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 508 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 5 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain H residue 63 GLN 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 J residue 56 HIS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 16 ILE 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 64 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 40 CYS 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 S residue 29 GLN Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain U residue 4 VAL 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: 6.9990 chunk 175 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS C 176 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS F 74 ASN J 56 HIS K 49 ASN K 110 GLN K 128 ASN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN O 7 GLN O 28 GLN O 37 GLN O 51 HIS P 15 ASN Q 65 ASN R 59 GLN T 68 HIS T 70 ASN T 71 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100492 restraints weight = 84893.520| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.07 r_work: 0.3037 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 48857 Z= 0.217 Angle : 0.696 13.878 72790 Z= 0.381 Chirality : 0.048 0.556 9274 Planarity : 0.006 0.074 4082 Dihedral : 24.884 177.827 23940 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.68 % Favored : 92.32 % Rotamer: Outliers : 5.58 % Allowed : 15.09 % Favored : 79.33 % 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: -1.92 (0.17), residues: 1900 helix: -0.14 (0.18), residues: 752 sheet: -1.40 (0.26), residues: 343 loop : -2.29 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 86 TYR 0.028 0.002 TYR J 13 PHE 0.025 0.002 PHE C 167 TRP 0.017 0.002 TRP C 18 HIS 0.011 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.22 (48853) covalent geometry : angle 0.69440 / 0.38 (72784) SS BOND : bond 0.01587 / 0.95 ( 3) SS BOND : angle 5.10980 / 5.52 ( 6) hydrogen bonds : bond 0.08771 / 9.66 ( 1374) hydrogen bonds : angle 4.60784 / 6.05 ( 2955) Misc. bond : bond 0.00577 / 0.29 ( 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: 91 poor density : 519 time to evaluate : 0.955 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: C 55 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8206 (tt0) REVERT: C 93 LEU cc_start: 0.7941 (mp) cc_final: 0.7660 (tp) REVERT: C 99 GLN cc_start: 0.6018 (tm-30) cc_final: 0.5752 (tm-30) REVERT: C 106 LYS cc_start: 0.8241 (mttp) cc_final: 0.7502 (mmmt) REVERT: C 142 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6527 (ttp80) REVERT: D 10 ARG cc_start: 0.7202 (ptt-90) cc_final: 0.6522 (tpt170) REVERT: D 125 VAL cc_start: 0.9397 (t) cc_final: 0.9090 (m) REVERT: E 63 ILE cc_start: 0.9204 (mt) cc_final: 0.8914 (mp) REVERT: G 52 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7108 (mt-10) REVERT: G 106 ASN cc_start: 0.8792 (m110) cc_final: 0.8569 (m-40) REVERT: I 47 GLN cc_start: 0.5820 (pm20) cc_final: 0.5546 (pm20) REVERT: I 61 ASN cc_start: 0.8540 (t0) cc_final: 0.8003 (m-40) REVERT: I 84 TYR cc_start: 0.7861 (m-80) cc_final: 0.7649 (m-80) REVERT: I 115 ARG cc_start: 0.7369 (ttm170) cc_final: 0.7157 (tmt170) REVERT: I 126 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8343 (ttt90) REVERT: J 11 LYS cc_start: 0.8471 (mttt) cc_final: 0.7752 (mtpp) REVERT: J 82 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7740 (tttt) REVERT: L 49 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7517 (mp) REVERT: L 73 ASN cc_start: 0.6763 (m-40) cc_final: 0.6408 (m-40) REVERT: L 89 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7818 (p0) REVERT: M 15 MET cc_start: 0.8460 (tpt) cc_final: 0.8042 (mmm) REVERT: M 16 GLU cc_start: 0.7858 (tt0) cc_final: 0.7435 (tt0) REVERT: M 31 ASN cc_start: 0.8421 (m-40) cc_final: 0.8036 (m110) REVERT: M 32 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8423 (tm-30) REVERT: M 83 GLU cc_start: 0.7915 (mp0) cc_final: 0.6496 (tp30) REVERT: M 90 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8760 (mp) REVERT: N 36 LYS cc_start: 0.8378 (tttp) cc_final: 0.8168 (tttp) REVERT: O 65 ARG cc_start: 0.8871 (mtt90) cc_final: 0.8528 (mtt90) REVERT: O 77 ARG cc_start: 0.8448 (mtp180) cc_final: 0.8088 (mtm-85) REVERT: P 17 GLN cc_start: 0.8784 (mp10) cc_final: 0.7492 (tp40) REVERT: P 44 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: P 50 GLN cc_start: 0.8196 (mt0) cc_final: 0.7865 (tm-30) REVERT: Q 19 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7731 (ttm-80) REVERT: R 47 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8909 (mtmt) REVERT: S 16 LEU cc_start: 0.8569 (tp) cc_final: 0.7993 (pp) REVERT: S 17 LYS cc_start: 0.7773 (tttt) cc_final: 0.7285 (tppt) REVERT: T 45 ASP cc_start: 0.7663 (m-30) cc_final: 0.7413 (t70) outliers start: 91 outliers final: 67 residues processed: 570 average time/residue: 0.3093 time to fit residues: 279.3617 Evaluate side-chains 559 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 486 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 105 VAL 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 105 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 62 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 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 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 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 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 126 ARG 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 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER 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 16 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 VAL 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 M residue 90 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 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 90 LEU Chi-restraints excluded: chain Q residue 91 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 104 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 212 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS K 78 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN M 88 GLN O 7 GLN Q 46 HIS Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097552 restraints weight = 85731.455| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.15 r_work: 0.2953 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3137 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= 0.341 Angle : 0.841 13.241 72790 Z= 0.438 Chirality : 0.057 0.646 9274 Planarity : 0.007 0.069 4082 Dihedral : 24.995 178.950 23937 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.79 % Favored : 91.26 % Rotamer: Outliers : 6.87 % Allowed : 17.55 % Favored : 75.58 % 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: -1.98 (0.18), residues: 1900 helix: -0.23 (0.18), residues: 750 sheet: -1.24 (0.26), residues: 340 loop : -2.36 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 32 TYR 0.025 0.003 TYR D 130 PHE 0.028 0.002 PHE H 10 TRP 0.018 0.003 TRP C 18 HIS 0.014 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.34 (48853) covalent geometry : angle 0.83938 / 0.44 (72784) SS BOND : bond 0.01144 / 0.57 ( 3) SS BOND : angle 5.16005 / 5.19 ( 6) hydrogen bonds : bond 0.09048 / 10.08 ( 1374) hydrogen bonds : angle 4.67732 / 6.18 ( 2955) Misc. bond : bond 0.00448 / 0.22 ( 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 610 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 498 time to evaluate : 0.970 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: 0.8594 (mt-10) cc_final: 0.8174 (tt0) REVERT: C 93 LEU cc_start: 0.7956 (mp) cc_final: 0.7692 (tp) REVERT: C 106 LYS cc_start: 0.8422 (mttp) cc_final: 0.7699 (mmmt) REVERT: C 161 GLU cc_start: 0.8210 (tp30) cc_final: 0.7754 (pm20) REVERT: D 10 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.6694 (tpt170) REVERT: D 125 VAL cc_start: 0.9444 (t) cc_final: 0.9212 (m) REVERT: D 126 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7328 (p0) REVERT: E 46 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9169 (m) REVERT: E 98 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7726 (ttm-80) REVERT: G 48 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7553 (mm-30) REVERT: G 52 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7767 (mt-10) REVERT: G 106 ASN cc_start: 0.8820 (m110) cc_final: 0.8546 (m-40) REVERT: H 13 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8350 (ttm110) REVERT: I 47 GLN cc_start: 0.6004 (OUTLIER) cc_final: 0.5589 (pm20) REVERT: I 58 TYR cc_start: 0.8232 (t80) cc_final: 0.7907 (t80) REVERT: I 61 ASN cc_start: 0.8626 (t0) cc_final: 0.8075 (t0) REVERT: I 115 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7105 (tmt170) REVERT: J 11 LYS cc_start: 0.8560 (mttt) cc_final: 0.7920 (mttm) REVERT: J 82 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7969 (tttt) REVERT: L 49 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7666 (mp) REVERT: L 89 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7814 (p0) REVERT: L 97 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9096 (mt) REVERT: M 15 MET cc_start: 0.8354 (tpt) cc_final: 0.8054 (mmm) REVERT: M 16 GLU cc_start: 0.7909 (tt0) cc_final: 0.7549 (tt0) REVERT: M 19 LEU cc_start: 0.9249 (mm) cc_final: 0.9038 (mm) REVERT: M 31 ASN cc_start: 0.8359 (m-40) cc_final: 0.8123 (m110) REVERT: M 32 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8565 (tm-30) REVERT: M 79 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7493 (mmt-90) REVERT: M 88 GLN cc_start: 0.8396 (tt0) cc_final: 0.8136 (tt0) REVERT: M 90 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8794 (mp) REVERT: N 47 MET cc_start: 0.8730 (mmt) cc_final: 0.8506 (mmt) REVERT: N 52 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: O 65 ARG cc_start: 0.9031 (mtt90) cc_final: 0.8761 (mtt90) REVERT: P 17 GLN cc_start: 0.8882 (mp10) cc_final: 0.7393 (tp40) REVERT: P 21 ILE cc_start: 0.9400 (mt) cc_final: 0.9167 (mt) REVERT: P 44 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: P 50 GLN cc_start: 0.8277 (mt0) cc_final: 0.8001 (tm-30) REVERT: P 96 LYS cc_start: 0.5586 (tmtt) cc_final: 0.5128 (tmtt) REVERT: R 47 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8970 (mtmt) REVERT: R 49 ARG cc_start: 0.9023 (ttm110) cc_final: 0.7964 (mtm-85) REVERT: S 16 LEU cc_start: 0.8545 (tp) cc_final: 0.7855 (pp) REVERT: S 17 LYS cc_start: 0.7795 (tttt) cc_final: 0.7307 (tppt) REVERT: T 30 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8961 (t) REVERT: T 45 ASP cc_start: 0.7843 (m-30) cc_final: 0.7476 (t70) outliers start: 112 outliers final: 81 residues processed: 557 average time/residue: 0.3078 time to fit residues: 271.3743 Evaluate side-chains 562 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 469 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 111 GLN 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 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 46 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 171 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 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 17 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 13 ARG 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 H residue 126 GLU Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 109 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 42 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL 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 40 THR Chi-restraints excluded: chain L residue 49 LEU 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 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 M residue 90 LEU Chi-restraints excluded: chain N residue 15 LYS 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 29 SER Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 33 THR 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 T residue 28 LEU Chi-restraints excluded: chain T residue 30 THR 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: 6.9990 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS D 54 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097991 restraints weight = 85012.076| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.08 r_work: 0.2994 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 48857 Z= 0.273 Angle : 0.740 13.683 72790 Z= 0.398 Chirality : 0.051 0.612 9274 Planarity : 0.006 0.057 4082 Dihedral : 24.973 179.927 23935 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.79 % Favored : 91.42 % Rotamer: Outliers : 7.42 % Allowed : 19.57 % Favored : 73.01 % 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: -1.75 (0.18), residues: 1900 helix: 0.07 (0.18), residues: 735 sheet: -1.10 (0.27), residues: 346 loop : -2.35 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 13 TYR 0.020 0.002 TYR Q 49 PHE 0.026 0.002 PHE H 10 TRP 0.017 0.002 TRP C 18 HIS 0.013 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.27 (48853) covalent geometry : angle 0.73898 / 0.40 (72784) SS BOND : bond 0.00936 / 0.49 ( 3) SS BOND : angle 4.92288 / 4.90 ( 6) hydrogen bonds : bond 0.08354 / 9.25 ( 1374) hydrogen bonds : angle 4.55808 / 6.06 ( 2955) Misc. bond : bond 0.00319 / 0.16 ( 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 613 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 492 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.8727 (t-90) REVERT: C 55 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8141 (tt0) REVERT: C 93 LEU cc_start: 0.8001 (mp) cc_final: 0.7693 (tp) REVERT: C 106 LYS cc_start: 0.8408 (mttp) cc_final: 0.7749 (mmmt) REVERT: C 109 GLU cc_start: 0.6083 (pt0) cc_final: 0.5798 (pt0) REVERT: C 142 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7526 (tmm-80) REVERT: C 161 GLU cc_start: 0.8170 (tp30) cc_final: 0.7753 (pm20) REVERT: C 188 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7152 (mt-10) REVERT: D 3 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.5677 (ttp80) REVERT: D 10 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.6718 (tpt170) REVERT: D 125 VAL cc_start: 0.9439 (t) cc_final: 0.9217 (m) REVERT: D 126 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7277 (p0) REVERT: D 146 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4978 (m-40) REVERT: E 153 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8020 (mt) REVERT: G 104 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8678 (tt) REVERT: H 13 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8116 (ttm110) REVERT: H 38 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8574 (mm-30) REVERT: I 47 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.5511 (pm20) REVERT: I 61 ASN cc_start: 0.8608 (t0) cc_final: 0.7830 (m-40) REVERT: I 115 ARG cc_start: 0.7427 (ttm170) cc_final: 0.7104 (tmt170) REVERT: J 11 LYS cc_start: 0.8542 (mttt) cc_final: 0.7915 (mttm) REVERT: L 49 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7600 (mp) REVERT: L 73 ASN cc_start: 0.7003 (p0) cc_final: 0.6478 (p0) REVERT: L 76 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7303 (mm-30) REVERT: L 89 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7873 (p0) REVERT: L 97 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9127 (mt) REVERT: L 109 ASN cc_start: 0.7716 (p0) cc_final: 0.7486 (p0) REVERT: M 16 GLU cc_start: 0.7879 (tt0) cc_final: 0.7514 (tt0) REVERT: M 31 ASN cc_start: 0.8281 (m-40) cc_final: 0.8008 (m110) REVERT: M 32 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8553 (tm-30) REVERT: M 67 GLU cc_start: 0.7740 (tp30) cc_final: 0.7460 (tp30) REVERT: M 88 GLN cc_start: 0.8293 (tt0) cc_final: 0.7992 (tt0) REVERT: M 90 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8780 (mp) REVERT: N 52 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: O 65 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8600 (mtt90) REVERT: P 17 GLN cc_start: 0.8818 (mp10) cc_final: 0.7346 (tp40) REVERT: P 21 ILE cc_start: 0.9393 (mt) cc_final: 0.9181 (mt) REVERT: P 44 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: P 50 GLN cc_start: 0.8230 (mt0) cc_final: 0.7950 (tm-30) REVERT: P 96 LYS cc_start: 0.5859 (tmtt) cc_final: 0.5366 (tmtt) REVERT: R 47 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8951 (mtmt) REVERT: R 49 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8446 (mtm110) REVERT: S 16 LEU cc_start: 0.8523 (tp) cc_final: 0.7806 (pp) REVERT: S 17 LYS cc_start: 0.7747 (tttt) cc_final: 0.7242 (tppt) REVERT: T 45 ASP cc_start: 0.7776 (m-30) cc_final: 0.7437 (t70) REVERT: T 54 THR cc_start: 0.9165 (m) cc_final: 0.8676 (p) outliers start: 121 outliers final: 84 residues processed: 556 average time/residue: 0.3026 time to fit residues: 268.8000 Evaluate side-chains 576 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 478 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 138 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 91 SER 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 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 176 LEU 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 171 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 82 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL 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 13 ARG Chi-restraints excluded: chain H residue 62 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 H residue 121 GLN Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 47 GLN 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 10 LEU 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 71 LYS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER 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 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET 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 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 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 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 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 11 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 51 LEU 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: 3.9990 chunk 157 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 264 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS I 57 ASN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100053 restraints weight = 84793.644| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.06 r_work: 0.3028 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48857 Z= 0.175 Angle : 0.625 13.745 72790 Z= 0.350 Chirality : 0.043 0.538 9274 Planarity : 0.005 0.054 4082 Dihedral : 24.881 179.544 23935 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.53 % Favored : 91.74 % Rotamer: Outliers : 6.32 % Allowed : 21.23 % Favored : 72.45 % 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: 0.33 (0.19), residues: 738 sheet: -1.04 (0.27), residues: 351 loop : -2.27 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 126 TYR 0.015 0.002 TYR Q 49 PHE 0.020 0.002 PHE H 10 TRP 0.019 0.001 TRP C 18 HIS 0.012 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (48853) covalent geometry : angle 0.62371 / 0.35 (72784) SS BOND : bond 0.01609 / 1.14 ( 3) SS BOND : angle 4.01534 / 3.90 ( 6) hydrogen bonds : bond 0.07511 / 8.25 ( 1374) hydrogen bonds : angle 4.36814 / 5.86 ( 2955) Misc. bond : bond 0.00132 / 0.07 ( 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 603 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 500 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8488 (t-90) REVERT: C 55 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8090 (tt0) REVERT: C 93 LEU cc_start: 0.8018 (mp) cc_final: 0.7717 (tp) REVERT: C 106 LYS cc_start: 0.8408 (mttp) cc_final: 0.7736 (mmmt) REVERT: C 161 GLU cc_start: 0.8128 (tp30) cc_final: 0.7683 (pm20) REVERT: D 10 ARG cc_start: 0.7357 (ptt-90) cc_final: 0.6619 (tpt170) REVERT: D 125 VAL cc_start: 0.9413 (t) cc_final: 0.9172 (m) REVERT: D 146 ASN cc_start: 0.5300 (OUTLIER) cc_final: 0.5072 (m-40) REVERT: E 36 TYR cc_start: 0.8162 (p90) cc_final: 0.7471 (p90) REVERT: E 93 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7827 (mtt180) REVERT: E 98 ARG cc_start: 0.7942 (ttt-90) cc_final: 0.7714 (ttm-80) REVERT: G 104 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8686 (tt) REVERT: H 13 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8099 (ttm110) REVERT: H 38 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8581 (mm-30) REVERT: I 47 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: I 61 ASN cc_start: 0.8697 (t0) cc_final: 0.7819 (m-40) REVERT: I 66 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7791 (pp30) REVERT: I 115 ARG cc_start: 0.7171 (ttm170) cc_final: 0.6898 (tmt170) REVERT: J 11 LYS cc_start: 0.8457 (mttt) cc_final: 0.7855 (mttm) REVERT: L 49 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7507 (mp) REVERT: L 76 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7540 (mm-30) REVERT: L 89 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7960 (p0) REVERT: L 109 ASN cc_start: 0.7756 (p0) cc_final: 0.7531 (p0) REVERT: M 16 GLU cc_start: 0.7795 (tt0) cc_final: 0.7426 (tt0) REVERT: M 31 ASN cc_start: 0.8222 (m-40) cc_final: 0.7968 (m110) REVERT: M 32 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8508 (tm-30) REVERT: M 79 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7571 (mmt180) REVERT: M 90 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8786 (mp) REVERT: N 52 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8543 (mm-30) REVERT: O 65 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8537 (mtt90) REVERT: P 17 GLN cc_start: 0.8835 (mp10) cc_final: 0.7471 (tp40) REVERT: P 44 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: P 50 GLN cc_start: 0.8180 (mt0) cc_final: 0.7916 (tm-30) REVERT: P 96 LYS cc_start: 0.5943 (tmtt) cc_final: 0.5471 (tmtt) REVERT: R 47 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8901 (mtmt) REVERT: R 49 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8426 (mtm110) REVERT: S 16 LEU cc_start: 0.8531 (tp) cc_final: 0.7839 (pp) REVERT: S 17 LYS cc_start: 0.7717 (tttt) cc_final: 0.7011 (tppt) REVERT: S 47 HIS cc_start: 0.8045 (t70) cc_final: 0.7365 (m-70) REVERT: T 45 ASP cc_start: 0.7924 (m-30) cc_final: 0.7652 (t0) REVERT: T 54 THR cc_start: 0.9021 (m) cc_final: 0.8568 (p) outliers start: 103 outliers final: 71 residues processed: 555 average time/residue: 0.3032 time to fit residues: 267.8743 Evaluate side-chains 559 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 477 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 42 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 MET 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 146 ASN Chi-restraints excluded: chain D residue 176 LEU 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 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 80 LEU Chi-restraints excluded: chain G residue 17 VAL 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 13 ARG Chi-restraints excluded: chain H residue 62 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 H residue 126 GLU 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 J residue 6 ILE Chi-restraints excluded: chain J residue 10 LEU 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 71 LYS 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 34 SER Chi-restraints excluded: chain K residue 88 VAL 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 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET 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 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 N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE 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 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 T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 106 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS D 54 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS I 57 ASN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN N 25 ASN O 7 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098754 restraints weight = 84829.915| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.07 r_work: 0.3007 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 48857 Z= 0.240 Angle : 0.699 13.515 72790 Z= 0.377 Chirality : 0.048 0.584 9274 Planarity : 0.006 0.056 4082 Dihedral : 24.832 177.869 23934 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.32 % Favored : 91.00 % Rotamer: Outliers : 6.99 % Allowed : 21.78 % Favored : 71.23 % 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: -1.54 (0.18), residues: 1900 helix: 0.33 (0.19), residues: 741 sheet: -1.02 (0.27), residues: 347 loop : -2.31 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 71 TYR 0.022 0.002 TYR F 54 PHE 0.020 0.002 PHE K 70 TRP 0.018 0.002 TRP C 18 HIS 0.011 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.24 (48853) covalent geometry : angle 0.69759 / 0.38 (72784) SS BOND : bond 0.00836 / 0.56 ( 3) SS BOND : angle 4.57288 / 4.47 ( 6) hydrogen bonds : bond 0.07801 / 8.56 ( 1374) hydrogen bonds : angle 4.39303 / 5.87 ( 2955) Misc. bond : bond 0.00141 / 0.07 ( 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 594 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 480 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8705 (t-90) REVERT: C 55 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8024 (tt0) REVERT: C 93 LEU cc_start: 0.8017 (mp) cc_final: 0.7721 (tp) REVERT: C 106 LYS cc_start: 0.8435 (mttp) cc_final: 0.7786 (mmmt) REVERT: C 138 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: C 161 GLU cc_start: 0.8117 (tp30) cc_final: 0.7684 (pm20) REVERT: D 3 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6129 (ttp80) REVERT: D 10 ARG cc_start: 0.7520 (ptt-90) cc_final: 0.6747 (tpt170) REVERT: D 125 VAL cc_start: 0.9437 (t) cc_final: 0.9196 (m) REVERT: D 126 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7253 (p0) REVERT: D 146 ASN cc_start: 0.5304 (OUTLIER) cc_final: 0.5072 (m-40) REVERT: E 36 TYR cc_start: 0.8159 (p90) cc_final: 0.7937 (p90) REVERT: E 45 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8255 (ttp80) REVERT: E 98 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7694 (ttm-80) REVERT: E 153 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8034 (mt) REVERT: F 54 TYR cc_start: 0.6930 (m-80) cc_final: 0.6662 (m-80) REVERT: G 104 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8707 (tt) REVERT: H 13 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8243 (ttm110) REVERT: H 38 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8537 (mm-30) REVERT: I 47 GLN cc_start: 0.5827 (OUTLIER) cc_final: 0.5353 (pm20) REVERT: I 61 ASN cc_start: 0.8632 (t0) cc_final: 0.8031 (m-40) REVERT: I 66 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: I 115 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6842 (tmt170) REVERT: J 11 LYS cc_start: 0.8466 (mttt) cc_final: 0.7862 (mttm) REVERT: K 82 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7977 (mtmm) REVERT: L 49 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7493 (mp) REVERT: L 76 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7663 (mm-30) REVERT: L 89 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8025 (p0) REVERT: L 97 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9049 (mt) REVERT: L 109 ASN cc_start: 0.7860 (p0) cc_final: 0.7635 (p0) REVERT: M 15 MET cc_start: 0.8350 (tpt) cc_final: 0.8101 (mmm) REVERT: M 16 GLU cc_start: 0.7805 (tt0) cc_final: 0.7416 (tt0) REVERT: M 31 ASN cc_start: 0.8205 (m-40) cc_final: 0.7958 (m110) REVERT: M 32 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8520 (tm-30) REVERT: M 79 ARG cc_start: 0.7672 (tpp-160) cc_final: 0.7407 (mmt180) REVERT: M 90 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8681 (mp) REVERT: M 101 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: N 52 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8560 (mm-30) REVERT: O 65 ARG cc_start: 0.8841 (mtt90) cc_final: 0.8573 (mtt90) REVERT: O 77 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8234 (ttm170) REVERT: P 17 GLN cc_start: 0.8820 (mp10) cc_final: 0.7365 (tp40) REVERT: P 44 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: P 50 GLN cc_start: 0.8204 (mt0) cc_final: 0.7928 (tm-30) REVERT: P 96 LYS cc_start: 0.5897 (tmtt) cc_final: 0.5386 (tmtt) REVERT: R 47 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8918 (mtmt) REVERT: R 49 ARG cc_start: 0.9083 (ttm110) cc_final: 0.8410 (mtm110) REVERT: S 16 LEU cc_start: 0.8486 (tp) cc_final: 0.7933 (pp) REVERT: S 17 LYS cc_start: 0.7643 (tttt) cc_final: 0.7148 (tppt) REVERT: T 45 ASP cc_start: 0.7926 (m-30) cc_final: 0.7666 (t0) REVERT: T 54 THR cc_start: 0.9050 (m) cc_final: 0.8577 (p) outliers start: 114 outliers final: 83 residues processed: 542 average time/residue: 0.2978 time to fit residues: 257.2439 Evaluate side-chains 563 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 463 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 138 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 176 LEU 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 8 LEU 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 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 62 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 H residue 126 GLU 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 10 LEU 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 73 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 88 VAL 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 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET 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 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 M residue 94 ARG Chi-restraints excluded: chain M residue 101 GLN Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 25 ASN 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 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 90 LEU Chi-restraints excluded: chain R residue 40 THR 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 77 THR Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 51 LEU 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: 0.7980 chunk 228 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 291 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 251 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 GLN C 68 HIS D 54 GLN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN O 7 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100881 restraints weight = 85208.441| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.06 r_work: 0.3042 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48857 Z= 0.158 Angle : 0.601 13.885 72790 Z= 0.338 Chirality : 0.041 0.522 9274 Planarity : 0.005 0.057 4082 Dihedral : 24.786 177.590 23934 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.63 % Favored : 91.68 % Rotamer: Outliers : 6.26 % Allowed : 22.88 % Favored : 70.86 % 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: -1.37 (0.19), residues: 1900 helix: 0.47 (0.19), residues: 743 sheet: -0.92 (0.27), residues: 347 loop : -2.25 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 71 TYR 0.023 0.002 TYR C 187 PHE 0.018 0.002 PHE K 70 TRP 0.019 0.001 TRP C 18 HIS 0.011 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (48853) covalent geometry : angle 0.59944 / 0.34 (72784) SS BOND : bond 0.00721 / 0.65 ( 3) SS BOND : angle 4.28721 / 4.65 ( 6) hydrogen bonds : bond 0.07210 / 7.88 ( 1374) hydrogen bonds : angle 4.23068 / 5.68 ( 2955) Misc. bond : bond 0.00157 / 0.08 ( 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 601 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 499 time to evaluate : 0.787 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 8 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8435 (t-90) REVERT: C 55 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7994 (tt0) REVERT: C 93 LEU cc_start: 0.8050 (mp) cc_final: 0.7648 (tp) REVERT: C 106 LYS cc_start: 0.8416 (mttp) cc_final: 0.7775 (mmmt) REVERT: C 161 GLU cc_start: 0.7897 (tp30) cc_final: 0.7542 (pm20) REVERT: D 3 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6142 (ttp80) REVERT: D 10 ARG cc_start: 0.7417 (ptt-90) cc_final: 0.6646 (tpt170) REVERT: E 36 TYR cc_start: 0.8137 (p90) cc_final: 0.7882 (p90) REVERT: E 45 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8026 (ttp80) REVERT: E 153 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8036 (mt) REVERT: G 104 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8680 (tt) REVERT: H 13 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8086 (ttm110) REVERT: H 38 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8509 (mm-30) REVERT: I 47 GLN cc_start: 0.5789 (OUTLIER) cc_final: 0.5300 (pm20) REVERT: I 61 ASN cc_start: 0.8628 (t0) cc_final: 0.7878 (m-40) REVERT: I 66 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7808 (pp30) REVERT: I 115 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6806 (tmt170) REVERT: J 11 LYS cc_start: 0.8359 (mttt) cc_final: 0.7790 (mttm) REVERT: L 49 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7461 (mp) REVERT: L 76 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7565 (mm-30) REVERT: L 89 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7982 (p0) REVERT: L 109 ASN cc_start: 0.7834 (p0) cc_final: 0.7607 (p0) REVERT: M 15 MET cc_start: 0.8313 (tpt) cc_final: 0.8056 (mmm) REVERT: M 16 GLU cc_start: 0.7861 (tt0) cc_final: 0.7432 (tt0) REVERT: M 31 ASN cc_start: 0.8181 (m-40) cc_final: 0.7907 (m110) REVERT: M 32 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8522 (tm-30) REVERT: M 79 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7433 (mmt-90) REVERT: M 90 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8670 (mp) REVERT: N 36 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8188 (pttp) REVERT: N 52 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: O 65 ARG cc_start: 0.8791 (mtt90) cc_final: 0.8557 (mtt90) REVERT: P 17 GLN cc_start: 0.8863 (mp10) cc_final: 0.7501 (tp40) REVERT: P 44 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: P 50 GLN cc_start: 0.8189 (mt0) cc_final: 0.7894 (tm-30) REVERT: P 90 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: P 96 LYS cc_start: 0.5923 (tmtt) cc_final: 0.5435 (tmtt) REVERT: R 47 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8863 (mtmt) REVERT: R 49 ARG cc_start: 0.9055 (ttm110) cc_final: 0.8408 (mtm110) REVERT: R 59 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: S 16 LEU cc_start: 0.8406 (tp) cc_final: 0.7858 (pp) REVERT: S 17 LYS cc_start: 0.7580 (tttt) cc_final: 0.7071 (tppt) REVERT: S 47 HIS cc_start: 0.8026 (t70) cc_final: 0.7357 (m-70) REVERT: T 45 ASP cc_start: 0.8073 (m-30) cc_final: 0.7672 (t0) REVERT: T 54 THR cc_start: 0.8988 (m) cc_final: 0.8532 (p) outliers start: 102 outliers final: 73 residues processed: 549 average time/residue: 0.3062 time to fit residues: 266.3540 Evaluate side-chains 568 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 480 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 42 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 5 THR 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 110 VAL Chi-restraints excluded: chain E residue 120 MET 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 8 LEU 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 17 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 126 GLU 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 10 LEU 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 71 LYS 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 34 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET 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 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU 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 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 51 LEU 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: 5.9990 chunk 210 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101311 restraints weight = 84374.004| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.04 r_work: 0.3049 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 48857 Z= 0.159 Angle : 0.600 13.728 72790 Z= 0.333 Chirality : 0.041 0.509 9274 Planarity : 0.005 0.057 4082 Dihedral : 24.692 177.388 23934 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.63 % Favored : 91.63 % Rotamer: Outliers : 6.01 % Allowed : 23.50 % Favored : 70.49 % 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: -1.20 (0.19), residues: 1900 helix: 0.62 (0.19), residues: 740 sheet: -0.87 (0.27), residues: 350 loop : -2.13 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 62 TYR 0.022 0.002 TYR C 187 PHE 0.022 0.002 PHE C 167 TRP 0.021 0.001 TRP C 18 HIS 0.010 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (48853) covalent geometry : angle 0.59834 / 0.33 (72784) SS BOND : bond 0.00230 / 0.21 ( 3) SS BOND : angle 4.29917 / 4.48 ( 6) hydrogen bonds : bond 0.07005 / 7.63 ( 1374) hydrogen bonds : angle 4.13955 / 5.54 ( 2955) Misc. bond : bond 0.00142 / 0.07 ( 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 584 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 486 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: symmetry clash revert: symmetry clash REVERT: C 8 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8357 (t-90) REVERT: C 55 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8084 (tt0) REVERT: C 93 LEU cc_start: 0.8026 (mp) cc_final: 0.7633 (tp) REVERT: C 106 LYS cc_start: 0.8427 (mttp) cc_final: 0.7775 (mmmt) REVERT: C 161 GLU cc_start: 0.7966 (tp30) cc_final: 0.7578 (pm20) REVERT: D 3 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6214 (ttp80) REVERT: D 10 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.6637 (tpt170) REVERT: E 71 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8525 (m) REVERT: E 153 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8048 (mt) REVERT: G 104 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8534 (tt) REVERT: H 13 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8103 (ttm110) REVERT: H 38 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8483 (mm-30) REVERT: I 47 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.5200 (pm20) REVERT: I 61 ASN cc_start: 0.8607 (t0) cc_final: 0.7860 (m-40) REVERT: I 66 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7796 (pp30) REVERT: I 115 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6769 (tmt170) REVERT: J 11 LYS cc_start: 0.8432 (mttt) cc_final: 0.7948 (mttm) REVERT: L 49 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7452 (mp) REVERT: L 76 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7535 (mm-30) REVERT: L 89 ASP cc_start: 0.8224 (m-30) cc_final: 0.7888 (p0) REVERT: L 97 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9095 (mm) REVERT: L 109 ASN cc_start: 0.8008 (p0) cc_final: 0.7780 (p0) REVERT: M 15 MET cc_start: 0.8297 (tpt) cc_final: 0.8083 (mmm) REVERT: M 16 GLU cc_start: 0.7903 (tt0) cc_final: 0.7462 (tt0) REVERT: M 31 ASN cc_start: 0.8345 (m-40) cc_final: 0.8039 (m110) REVERT: M 32 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8494 (tm-30) REVERT: M 79 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7512 (mmt-90) REVERT: M 90 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (mp) REVERT: N 36 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8181 (pttp) REVERT: N 52 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: O 65 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8534 (mtt90) REVERT: P 17 GLN cc_start: 0.8848 (mp10) cc_final: 0.7518 (tp40) REVERT: P 44 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: P 50 GLN cc_start: 0.8176 (mt0) cc_final: 0.7893 (tm-30) REVERT: P 90 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: P 96 LYS cc_start: 0.6011 (tmtt) cc_final: 0.5536 (tmtt) REVERT: R 47 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8804 (mtmt) REVERT: R 49 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8436 (mtm110) REVERT: S 16 LEU cc_start: 0.8367 (tp) cc_final: 0.7797 (pp) REVERT: S 17 LYS cc_start: 0.7627 (tttt) cc_final: 0.7139 (tppt) REVERT: S 47 HIS cc_start: 0.7957 (t70) cc_final: 0.7152 (m-70) REVERT: T 54 THR cc_start: 0.8978 (m) cc_final: 0.8530 (p) outliers start: 98 outliers final: 75 residues processed: 531 average time/residue: 0.3115 time to fit residues: 261.5604 Evaluate side-chains 563 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 473 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 133 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 5 THR 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 71 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 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 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL 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 13 ARG Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 126 GLU 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 10 LEU Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 71 LYS 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 88 VAL 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 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 97 ILE 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 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LYS 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 O residue 73 VAL Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 51 LEU 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: 20.0000 chunk 172 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 310 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS I 64 HIS I 146 GLN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN O 7 GLN R 59 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104468 restraints weight = 84796.053| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.03 r_work: 0.3102 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 48857 Z= 0.118 Angle : 0.551 14.125 72790 Z= 0.313 Chirality : 0.037 0.449 9274 Planarity : 0.004 0.057 4082 Dihedral : 24.625 178.573 23934 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.00 % Favored : 92.32 % Rotamer: Outliers : 4.91 % Allowed : 24.66 % 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: -1.01 (0.19), residues: 1900 helix: 0.83 (0.19), residues: 742 sheet: -0.88 (0.27), residues: 359 loop : -2.02 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 112 TYR 0.025 0.001 TYR C 187 PHE 0.021 0.002 PHE C 167 TRP 0.020 0.001 TRP C 18 HIS 0.013 0.001 HIS I 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (48853) covalent geometry : angle 0.54991 / 0.31 (72784) SS BOND : bond 0.01306 / 1.03 ( 3) SS BOND : angle 4.10196 / 4.24 ( 6) hydrogen bonds : bond 0.06585 / 7.13 ( 1374) hydrogen bonds : angle 4.04622 / 5.42 ( 2955) Misc. bond : bond 0.00157 / 0.08 ( 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 571 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 491 time to evaluate : 0.954 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: C 93 LEU cc_start: 0.8015 (mp) cc_final: 0.7644 (tp) REVERT: C 106 LYS cc_start: 0.8353 (mttp) cc_final: 0.7741 (mmmt) REVERT: C 161 GLU cc_start: 0.7991 (tp30) cc_final: 0.7621 (pm20) REVERT: D 3 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6126 (ttp80) REVERT: D 10 ARG cc_start: 0.7143 (ptt-90) cc_final: 0.6529 (tpt170) REVERT: E 153 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7935 (mt) REVERT: G 104 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8475 (tt) REVERT: H 116 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7176 (mmp-170) REVERT: I 47 GLN cc_start: 0.5793 (OUTLIER) cc_final: 0.5241 (pm20) REVERT: I 61 ASN cc_start: 0.8560 (t0) cc_final: 0.8082 (m-40) REVERT: I 115 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6780 (tmt170) REVERT: J 11 LYS cc_start: 0.8438 (mttt) cc_final: 0.7995 (mttm) REVERT: J 24 LYS cc_start: 0.7495 (ttmt) cc_final: 0.7262 (ttmm) REVERT: L 49 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7417 (mp) REVERT: L 76 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7476 (mm-30) REVERT: L 89 ASP cc_start: 0.8079 (m-30) cc_final: 0.7777 (p0) REVERT: M 15 MET cc_start: 0.8221 (tpt) cc_final: 0.8012 (mmm) REVERT: M 16 GLU cc_start: 0.7855 (tt0) cc_final: 0.7357 (tt0) REVERT: M 31 ASN cc_start: 0.8315 (m-40) cc_final: 0.7940 (m110) REVERT: M 32 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8475 (tm-30) REVERT: M 79 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7539 (mmt-90) REVERT: M 90 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8698 (mp) REVERT: N 52 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: O 10 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7223 (mp0) REVERT: O 65 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8440 (mtt90) REVERT: P 17 GLN cc_start: 0.8803 (mp10) cc_final: 0.7574 (tp-100) REVERT: P 44 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: P 50 GLN cc_start: 0.8176 (mt0) cc_final: 0.7930 (tm-30) REVERT: P 90 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: P 96 LYS cc_start: 0.5790 (tmtt) cc_final: 0.5421 (tmtt) REVERT: R 47 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8756 (mtmt) REVERT: R 49 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8550 (mtm110) REVERT: S 16 LEU cc_start: 0.8351 (tp) cc_final: 0.7821 (pp) REVERT: S 17 LYS cc_start: 0.7537 (tttt) cc_final: 0.7083 (tppt) REVERT: S 47 HIS cc_start: 0.8041 (t70) cc_final: 0.7372 (m-70) REVERT: T 45 ASP cc_start: 0.8061 (m-30) cc_final: 0.7615 (t70) REVERT: T 54 THR cc_start: 0.8943 (m) cc_final: 0.8545 (p) outliers start: 80 outliers final: 61 residues processed: 527 average time/residue: 0.3134 time to fit residues: 260.7270 Evaluate side-chains 548 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 478 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET 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 65 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 54 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 71 LYS 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 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 115 SER 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 M residue 94 ARG Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 25 ASN 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 O residue 73 VAL Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 VAL 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 28 LEU Chi-restraints excluded: chain T residue 51 LEU 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: 0.0870 chunk 209 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 10.9990 chunk 54 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 overall best weight: 2.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 HIS G 106 ASN I 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102166 restraints weight = 85073.505| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.05 r_work: 0.3065 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48857 Z= 0.173 Angle : 0.611 13.267 72790 Z= 0.334 Chirality : 0.042 0.509 9274 Planarity : 0.005 0.077 4082 Dihedral : 24.570 177.182 23933 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.79 % Favored : 91.53 % Rotamer: Outliers : 4.54 % Allowed : 25.15 % Favored : 70.31 % 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: -1.04 (0.19), residues: 1900 helix: 0.79 (0.19), residues: 746 sheet: -0.87 (0.27), residues: 357 loop : -2.05 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 23 TYR 0.024 0.002 TYR C 187 PHE 0.024 0.002 PHE C 167 TRP 0.019 0.002 TRP C 18 HIS 0.009 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (48853) covalent geometry : angle 0.60860 / 0.33 (72784) SS BOND : bond 0.01438 / 1.04 ( 3) SS BOND : angle 5.50856 / 6.12 ( 6) hydrogen bonds : bond 0.06870 / 7.46 ( 1374) hydrogen bonds : angle 4.07199 / 5.44 ( 2955) Misc. bond : bond 0.00155 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11782.18 seconds wall clock time: 202 minutes 31.01 seconds (12151.01 seconds total)