Starting phenix.real_space_refine on Fri Feb 16 23:06:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3o_6880/02_2024/5z3o_6880_updated.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 294 5.49 5 Mg 1 5.21 5 S 29 5.16 5 C 9675 2.51 5 N 3095 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 83": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "O TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 898": "NH1" <-> "NH2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1142": "NH1" <-> "NH2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1268": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16802 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4791 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 580, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563, None: 2} Not linked: pdbres="GLY O1348 " pdbres="ADP O1501 " Not linked: pdbres="ADP O1501 " pdbres=" MG O1502 " Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.30, per 1000 atoms: 0.55 Number of scatterers: 16802 At special positions: 0 Unit cell: (149.16, 117.48, 135.96, 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 29 16.00 P 294 15.00 Mg 1 11.99 O 3708 8.00 N 3095 7.00 C 9675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 2 sheets defined 56.3% alpha, 1.9% beta 114 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 8.71 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.920A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.891A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.797A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.745A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.792A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.920A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 removed outlier: 3.892A pdb=" N ARG E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.746A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 119 removed outlier: 3.793A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 112 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 672 through 682 Processing helix chain 'O' and resid 684 through 689 Processing helix chain 'O' and resid 744 through 749 removed outlier: 3.719A pdb=" N VAL O 747 " --> pdb=" O TYR O 744 " (cutoff:3.500A) Processing helix chain 'O' and resid 769 through 784 removed outlier: 3.640A pdb=" N ASN O 784 " --> pdb=" O SER O 780 " (cutoff:3.500A) Processing helix chain 'O' and resid 798 through 811 Processing helix chain 'O' and resid 825 through 837 removed outlier: 4.241A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA O 836 " --> pdb=" O SER O 832 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS O 837 " --> pdb=" O SER O 833 " (cutoff:3.500A) Processing helix chain 'O' and resid 850 through 862 removed outlier: 3.984A pdb=" N ALA O 856 " --> pdb=" O ASN O 852 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS O 857 " --> pdb=" O GLU O 853 " (cutoff:3.500A) Processing helix chain 'O' and resid 874 through 878 Processing helix chain 'O' and resid 880 through 885 Processing helix chain 'O' and resid 896 through 899 No H-bonds generated for 'chain 'O' and resid 896 through 899' Processing helix chain 'O' and resid 905 through 911 Processing helix chain 'O' and resid 943 through 957 removed outlier: 4.237A pdb=" N ASN O 947 " --> pdb=" O PRO O 943 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS O 950 " --> pdb=" O PHE O 946 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER O 951 " --> pdb=" O ASN O 947 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE O 952 " --> pdb=" O SER O 948 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP O 953 " --> pdb=" O VAL O 949 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU O 954 " --> pdb=" O LYS O 950 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP O 955 " --> pdb=" O SER O 951 " (cutoff:3.500A) Processing helix chain 'O' and resid 969 through 972 No H-bonds generated for 'chain 'O' and resid 969 through 972' Processing helix chain 'O' and resid 976 through 986 Processing helix chain 'O' and resid 996 through 998 No H-bonds generated for 'chain 'O' and resid 996 through 998' Processing helix chain 'O' and resid 1021 through 1030 Processing helix chain 'O' and resid 1050 through 1058 removed outlier: 4.055A pdb=" N LEU O1055 " --> pdb=" O GLN O1051 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) Processing helix chain 'O' and resid 1069 through 1072 No H-bonds generated for 'chain 'O' and resid 1069 through 1072' Processing helix chain 'O' and resid 1083 through 1085 No H-bonds generated for 'chain 'O' and resid 1083 through 1085' Processing helix chain 'O' and resid 1087 through 1102 removed outlier: 4.327A pdb=" N LEU O1091 " --> pdb=" O GLY O1087 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O1092 " --> pdb=" O LYS O1088 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1125 Processing helix chain 'O' and resid 1140 through 1149 removed outlier: 3.918A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1187 through 1198 removed outlier: 3.789A pdb=" N LEU O1191 " --> pdb=" O HIS O1188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN O1192 " --> pdb=" O GLN O1189 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA O1193 " --> pdb=" O ASP O1190 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN O1194 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS O1198 " --> pdb=" O ASP O1195 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1226 Processing helix chain 'O' and resid 1230 through 1240 removed outlier: 3.565A pdb=" N ILE O1236 " --> pdb=" O GLY O1233 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN O1237 " --> pdb=" O LYS O1234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY O1239 " --> pdb=" O ILE O1236 " (cutoff:3.500A) Processing helix chain 'O' and resid 1247 through 1249 No H-bonds generated for 'chain 'O' and resid 1247 through 1249' Processing helix chain 'O' and resid 1252 through 1262 removed outlier: 4.221A pdb=" N ALA O1260 " --> pdb=" O SER O1256 " (cutoff:3.500A) Processing helix chain 'O' and resid 1265 through 1267 No H-bonds generated for 'chain 'O' and resid 1265 through 1267' Processing helix chain 'O' and resid 1280 through 1287 removed outlier: 4.335A pdb=" N LEU O1287 " --> pdb=" O ILE O1283 " (cutoff:3.500A) Processing helix chain 'O' and resid 1291 through 1306 removed outlier: 3.625A pdb=" N VAL O1296 " --> pdb=" O GLU O1292 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS O1306 " --> pdb=" O GLU O1302 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1340 No H-bonds generated for 'chain 'O' and resid 1337 through 1340' Processing helix chain 'O' and resid 1342 through 1345 No H-bonds generated for 'chain 'O' and resid 1342 through 1345' Processing sheet with id= A, first strand: chain 'O' and resid 788 through 790 removed outlier: 3.922A pdb=" N GLY O 788 " --> pdb=" O ARG O 919 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE O 921 " --> pdb=" O GLY O 788 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU O 790 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 922 " --> pdb=" O ILE O 893 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'O' and resid 1159 through 1162 removed outlier: 6.323A pdb=" N THR O1177 " --> pdb=" O LEU O1107 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE O1109 " --> pdb=" O THR O1177 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE O1179 " --> pdb=" O PHE O1109 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG O1207 " --> pdb=" O VAL O1178 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE O1180 " --> pdb=" O ARG O1207 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU O1209 " --> pdb=" O ILE O1180 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 8.34 Time building geometry restraints manager: 9.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3371 1.33 - 1.45: 5070 1.45 - 1.57: 8607 1.57 - 1.69: 585 1.69 - 1.81: 53 Bond restraints: 17686 Sorted by residual: bond pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" C ARG A 131 " pdb=" O ARG A 131 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.29e-02 6.01e+03 2.07e+00 bond pdb=" C ASP E 106 " pdb=" O ASP E 106 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.05e+00 bond pdb=" C3' DA J 14 " pdb=" O3' DA J 14 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" C3' DG J 137 " pdb=" O3' DG J 137 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 17681 not shown) Histogram of bond angle deviations from ideal: 97.59 - 105.28: 1341 105.28 - 112.96: 10058 112.96 - 120.65: 8255 120.65 - 128.34: 5115 128.34 - 136.02: 359 Bond angle restraints: 25128 Sorted by residual: angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.17e+01 angle pdb=" C ILE O1058 " pdb=" N CYS O1059 " pdb=" CA CYS O1059 " ideal model delta sigma weight residual 122.06 116.26 5.80 1.86e+00 2.89e-01 9.73e+00 angle pdb=" C ILE O 815 " pdb=" N ARG O 816 " pdb=" CA ARG O 816 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.72e+00 angle pdb=" CA LEU O 927 " pdb=" CB LEU O 927 " pdb=" CG LEU O 927 " ideal model delta sigma weight residual 116.30 126.54 -10.24 3.50e+00 8.16e-02 8.55e+00 angle pdb=" C3' DG I 128 " pdb=" C2' DG I 128 " pdb=" C1' DG I 128 " ideal model delta sigma weight residual 101.60 97.59 4.01 1.50e+00 4.44e-01 7.15e+00 ... (remaining 25123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8659 35.72 - 71.44: 1259 71.44 - 107.16: 20 107.16 - 142.88: 2 142.88 - 178.60: 7 Dihedral angle restraints: 9947 sinusoidal: 6016 harmonic: 3931 Sorted by residual: dihedral pdb=" CA PRO O 932 " pdb=" C PRO O 932 " pdb=" N GLU O 933 " pdb=" CA GLU O 933 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA HIS O 913 " pdb=" C HIS O 913 " pdb=" N TYR O 914 " pdb=" CA TYR O 914 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU O1258 " pdb=" C LEU O1258 " pdb=" N ASP O1259 " pdb=" CA ASP O1259 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 9944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2460 0.051 - 0.102: 332 0.102 - 0.153: 60 0.153 - 0.204: 8 0.204 - 0.255: 3 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CG LEU O1258 " pdb=" CB LEU O1258 " pdb=" CD1 LEU O1258 " pdb=" CD2 LEU O1258 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU O1222 " pdb=" CB LEU O1222 " pdb=" CD1 LEU O1222 " pdb=" CD2 LEU O1222 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2860 not shown) Planarity restraints: 2167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.027 2.00e-02 2.50e+03 1.36e-02 5.06e+00 pdb=" N9 DA I 39 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.025 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO E 121 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 121 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.027 5.00e-02 4.00e+02 ... (remaining 2164 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 298 2.62 - 3.19: 14814 3.19 - 3.76: 29425 3.76 - 4.33: 38961 4.33 - 4.90: 56609 Nonbonded interactions: 140107 Sorted by model distance: nonbonded pdb=" O1B ADP O1501 " pdb="MG MG O1502 " model vdw 2.055 2.170 nonbonded pdb=" O1A ADP O1501 " pdb="MG MG O1502 " model vdw 2.065 2.170 nonbonded pdb=" O ALA O 748 " pdb=" ND2 ASN O 784 " model vdw 2.205 2.520 nonbonded pdb=" OP1 DA I 97 " pdb=" ND2 ASN O1186 " model vdw 2.230 2.520 nonbonded pdb=" O LEU O 971 " pdb=" OG1 THR O 976 " model vdw 2.236 2.440 ... (remaining 140102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 57.150 Find NCS groups from input model: 0.660 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.003 0.044 17686 Z= 0.186 Angle : 0.634 10.236 25128 Z= 0.363 Chirality : 0.038 0.255 2863 Planarity : 0.004 0.048 2167 Dihedral : 24.397 178.604 7393 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 0.44 % Allowed : 1.74 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.19), residues: 1316 helix: -2.37 (0.15), residues: 742 sheet: -2.49 (0.55), residues: 65 loop : -2.07 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O1083 HIS 0.004 0.001 HIS O 913 PHE 0.022 0.002 PHE O1241 TYR 0.018 0.002 TYR F 98 ARG 0.004 0.001 ARG O 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 454 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7457 (mtt-85) REVERT: A 59 GLU cc_start: 0.8859 (pt0) cc_final: 0.8504 (mm-30) REVERT: B 82 THR cc_start: 0.9479 (p) cc_final: 0.9205 (p) REVERT: D 51 ILE cc_start: 0.8053 (tt) cc_final: 0.7778 (tt) REVERT: E 60 LEU cc_start: 0.8606 (tp) cc_final: 0.7926 (tp) REVERT: F 80 THR cc_start: 0.9092 (m) cc_final: 0.8892 (p) REVERT: G 90 ASP cc_start: 0.8364 (t0) cc_final: 0.8114 (t0) REVERT: O 806 LEU cc_start: 0.8832 (mt) cc_final: 0.8630 (mt) REVERT: O 891 MET cc_start: 0.6384 (ptp) cc_final: 0.6108 (ptp) REVERT: O 895 GLU cc_start: 0.7322 (tp30) cc_final: 0.7101 (tp30) REVERT: O 1184 ASP cc_start: 0.7980 (m-30) cc_final: 0.6869 (m-30) REVERT: O 1188 HIS cc_start: 0.7937 (p-80) cc_final: 0.7449 (p-80) REVERT: O 1222 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8474 (tm) outliers start: 5 outliers final: 3 residues processed: 457 average time/residue: 0.3897 time to fit residues: 243.2143 Evaluate side-chains 242 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 25 ASN C 73 ASN E 68 GLN E 125 GLN G 38 ASN G 73 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** O 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17686 Z= 0.359 Angle : 0.748 10.259 25128 Z= 0.404 Chirality : 0.043 0.363 2863 Planarity : 0.006 0.053 2167 Dihedral : 29.779 177.361 4690 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.79 % Allowed : 13.75 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1316 helix: -0.79 (0.17), residues: 783 sheet: -2.20 (0.61), residues: 64 loop : -2.00 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O1083 HIS 0.008 0.002 HIS O 897 PHE 0.021 0.003 PHE O 946 TYR 0.025 0.003 TYR O 745 ARG 0.009 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 1.681 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: B 74 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8650 (tm-30) REVERT: C 64 GLU cc_start: 0.8918 (tt0) cc_final: 0.8586 (pt0) REVERT: C 72 ASP cc_start: 0.8751 (m-30) cc_final: 0.8449 (m-30) REVERT: F 25 ASN cc_start: 0.6721 (m-40) cc_final: 0.6208 (m-40) REVERT: F 27 GLN cc_start: 0.8937 (pp30) cc_final: 0.8683 (pp30) REVERT: F 80 THR cc_start: 0.9198 (m) cc_final: 0.8902 (p) REVERT: H 80 TYR cc_start: 0.8057 (m-10) cc_final: 0.7577 (m-10) REVERT: H 102 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7661 (tm-30) REVERT: H 103 LEU cc_start: 0.9032 (tp) cc_final: 0.8770 (tp) REVERT: O 760 SER cc_start: 0.9060 (m) cc_final: 0.8826 (p) REVERT: O 894 ASP cc_start: 0.8626 (t70) cc_final: 0.8378 (t70) REVERT: O 1025 GLN cc_start: 0.7503 (tt0) cc_final: 0.7106 (mt0) REVERT: O 1112 MET cc_start: 0.7997 (mmt) cc_final: 0.7750 (mmm) REVERT: O 1184 ASP cc_start: 0.8130 (m-30) cc_final: 0.7834 (m-30) outliers start: 55 outliers final: 33 residues processed: 286 average time/residue: 0.3357 time to fit residues: 136.2845 Evaluate side-chains 229 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 890 HIS Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1248 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 0.0570 chunk 128 optimal weight: 8.9990 chunk 142 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 93 GLN G 38 ASN G 73 ASN H 46 HIS O 749 HIS ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17686 Z= 0.186 Angle : 0.624 10.373 25128 Z= 0.341 Chirality : 0.037 0.194 2863 Planarity : 0.004 0.048 2167 Dihedral : 29.570 177.752 4686 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.26 % Allowed : 15.49 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1316 helix: 0.10 (0.19), residues: 777 sheet: -1.69 (0.61), residues: 64 loop : -1.67 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 777 HIS 0.005 0.001 HIS O 913 PHE 0.018 0.002 PHE O 946 TYR 0.022 0.002 TYR B 98 ARG 0.006 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 1.592 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: A 54 TYR cc_start: 0.8413 (m-80) cc_final: 0.8171 (m-80) REVERT: B 84 MET cc_start: 0.9117 (mmm) cc_final: 0.8880 (mmm) REVERT: B 98 TYR cc_start: 0.8637 (m-80) cc_final: 0.8346 (m-80) REVERT: C 64 GLU cc_start: 0.8884 (tt0) cc_final: 0.8639 (pt0) REVERT: C 72 ASP cc_start: 0.8793 (m-30) cc_final: 0.8484 (m-30) REVERT: F 25 ASN cc_start: 0.6627 (m-40) cc_final: 0.6104 (m-40) REVERT: F 27 GLN cc_start: 0.8912 (pp30) cc_final: 0.8608 (pp30) REVERT: F 63 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: F 80 THR cc_start: 0.9093 (m) cc_final: 0.8800 (p) REVERT: H 32 GLU cc_start: 0.7983 (tp30) cc_final: 0.7517 (tp30) REVERT: H 102 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7433 (tm-30) REVERT: O 760 SER cc_start: 0.9026 (m) cc_final: 0.8782 (p) REVERT: O 1026 MET cc_start: 0.6666 (mtt) cc_final: 0.4782 (mmm) REVERT: O 1052 ILE cc_start: 0.8280 (mm) cc_final: 0.8069 (mp) REVERT: O 1055 LEU cc_start: 0.8298 (mt) cc_final: 0.8016 (mt) REVERT: O 1112 MET cc_start: 0.8081 (mmt) cc_final: 0.7805 (tpp) REVERT: O 1184 ASP cc_start: 0.7973 (m-30) cc_final: 0.7743 (m-30) outliers start: 49 outliers final: 30 residues processed: 260 average time/residue: 0.3287 time to fit residues: 122.8099 Evaluate side-chains 239 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN E 68 GLN G 38 ASN G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17686 Z= 0.312 Angle : 0.684 17.072 25128 Z= 0.373 Chirality : 0.040 0.184 2863 Planarity : 0.005 0.047 2167 Dihedral : 29.958 179.008 4686 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 5.74 % Allowed : 14.88 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1316 helix: 0.23 (0.19), residues: 780 sheet: -1.40 (0.63), residues: 66 loop : -1.41 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 777 HIS 0.007 0.001 HIS O 897 PHE 0.017 0.002 PHE O1063 TYR 0.025 0.002 TYR H 80 ARG 0.005 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 200 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8908 (tt0) cc_final: 0.8694 (pt0) REVERT: C 72 ASP cc_start: 0.8842 (m-30) cc_final: 0.8588 (m-30) REVERT: D 44 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8959 (tm-30) REVERT: E 107 THR cc_start: 0.9309 (m) cc_final: 0.9053 (t) REVERT: F 25 ASN cc_start: 0.6883 (m-40) cc_final: 0.6314 (m-40) REVERT: F 27 GLN cc_start: 0.8943 (pp30) cc_final: 0.8550 (pp30) REVERT: F 63 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: F 80 THR cc_start: 0.9233 (m) cc_final: 0.8872 (p) REVERT: G 113 SER cc_start: 0.8802 (m) cc_final: 0.8477 (t) REVERT: O 760 SER cc_start: 0.9097 (m) cc_final: 0.8866 (p) REVERT: O 1015 MET cc_start: 0.7814 (mmt) cc_final: 0.7530 (mmt) REVERT: O 1052 ILE cc_start: 0.8276 (mm) cc_final: 0.8047 (mp) REVERT: O 1112 MET cc_start: 0.8352 (mmt) cc_final: 0.8133 (mmm) REVERT: O 1119 MET cc_start: 0.9111 (tpp) cc_final: 0.8906 (tpp) REVERT: O 1300 MET cc_start: 0.7364 (ttm) cc_final: 0.6556 (ptm) outliers start: 66 outliers final: 44 residues processed: 243 average time/residue: 0.3100 time to fit residues: 109.9050 Evaluate side-chains 228 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS G 73 ASN G 112 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17686 Z= 0.342 Angle : 0.695 12.000 25128 Z= 0.379 Chirality : 0.040 0.188 2863 Planarity : 0.005 0.050 2167 Dihedral : 30.018 179.990 4686 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 5.83 % Allowed : 17.49 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1316 helix: 0.31 (0.19), residues: 781 sheet: -1.37 (0.63), residues: 66 loop : -1.46 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 777 HIS 0.006 0.001 HIS O 913 PHE 0.023 0.002 PHE O1063 TYR 0.041 0.002 TYR H 80 ARG 0.007 0.001 ARG O1084 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 198 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9270 (mmm) cc_final: 0.9065 (tpt) REVERT: C 64 GLU cc_start: 0.8920 (tt0) cc_final: 0.8659 (pt0) REVERT: C 72 ASP cc_start: 0.8855 (m-30) cc_final: 0.8584 (m-30) REVERT: D 44 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8948 (tm-30) REVERT: E 120 MET cc_start: 0.7214 (mtm) cc_final: 0.6881 (mtm) REVERT: F 25 ASN cc_start: 0.6763 (m-40) cc_final: 0.6227 (m-40) REVERT: F 27 GLN cc_start: 0.8868 (pp30) cc_final: 0.8465 (pp30) REVERT: F 63 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8428 (mt-10) REVERT: F 80 THR cc_start: 0.9222 (m) cc_final: 0.8870 (p) REVERT: H 32 GLU cc_start: 0.8069 (tp30) cc_final: 0.7618 (tp30) REVERT: O 760 SER cc_start: 0.9097 (m) cc_final: 0.8889 (p) REVERT: O 895 GLU cc_start: 0.8075 (tp30) cc_final: 0.7793 (tp30) REVERT: O 1052 ILE cc_start: 0.8280 (mm) cc_final: 0.8074 (mp) outliers start: 67 outliers final: 50 residues processed: 240 average time/residue: 0.2996 time to fit residues: 105.7221 Evaluate side-chains 238 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 825 LEU Chi-restraints excluded: chain O residue 877 ILE Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN G 38 ASN G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN O1347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17686 Z= 0.179 Angle : 0.625 10.435 25128 Z= 0.342 Chirality : 0.036 0.208 2863 Planarity : 0.004 0.051 2167 Dihedral : 29.739 179.617 4686 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 4.09 % Allowed : 18.97 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1316 helix: 0.71 (0.20), residues: 766 sheet: -1.10 (0.64), residues: 66 loop : -1.41 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 777 HIS 0.006 0.001 HIS O 913 PHE 0.022 0.001 PHE O1063 TYR 0.036 0.002 TYR H 80 ARG 0.006 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8863 (tt0) cc_final: 0.8595 (pt0) REVERT: C 72 ASP cc_start: 0.8748 (m-30) cc_final: 0.8471 (m-30) REVERT: D 105 LYS cc_start: 0.8744 (ptmm) cc_final: 0.8463 (pttm) REVERT: F 25 ASN cc_start: 0.6651 (m-40) cc_final: 0.6170 (m-40) REVERT: F 27 GLN cc_start: 0.8867 (pp30) cc_final: 0.8566 (pp30) REVERT: F 63 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8367 (mt-10) REVERT: F 80 THR cc_start: 0.9123 (m) cc_final: 0.8818 (p) REVERT: G 92 GLU cc_start: 0.8785 (pp20) cc_final: 0.7858 (pp20) REVERT: O 760 SER cc_start: 0.8953 (m) cc_final: 0.8742 (p) REVERT: O 1223 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8843 (mm-30) outliers start: 47 outliers final: 29 residues processed: 247 average time/residue: 0.3109 time to fit residues: 112.4766 Evaluate side-chains 226 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1223 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 chunk 87 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17686 Z= 0.375 Angle : 0.720 10.990 25128 Z= 0.390 Chirality : 0.041 0.202 2863 Planarity : 0.005 0.057 2167 Dihedral : 30.112 179.331 4686 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 5.13 % Allowed : 19.84 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1316 helix: 0.50 (0.19), residues: 780 sheet: -1.17 (0.65), residues: 66 loop : -1.34 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 777 HIS 0.009 0.001 HIS O 913 PHE 0.022 0.002 PHE O1063 TYR 0.061 0.003 TYR H 80 ARG 0.010 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9176 (mmm) cc_final: 0.8908 (tpp) REVERT: C 64 GLU cc_start: 0.8909 (tt0) cc_final: 0.8648 (pt0) REVERT: C 72 ASP cc_start: 0.8778 (m-30) cc_final: 0.8492 (m-30) REVERT: F 25 ASN cc_start: 0.6751 (m-40) cc_final: 0.6263 (m-40) REVERT: F 27 GLN cc_start: 0.8936 (pp30) cc_final: 0.8515 (pp30) REVERT: F 63 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8376 (mt-10) REVERT: F 80 THR cc_start: 0.9212 (m) cc_final: 0.8949 (p) REVERT: G 90 ASP cc_start: 0.8471 (t0) cc_final: 0.8261 (t0) REVERT: O 750 ARG cc_start: 0.6693 (ptt-90) cc_final: 0.5453 (mmt90) REVERT: O 835 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: O 1026 MET cc_start: 0.7296 (ptp) cc_final: 0.5428 (mmm) REVERT: O 1223 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8838 (mm-30) outliers start: 59 outliers final: 45 residues processed: 230 average time/residue: 0.2879 time to fit residues: 97.5135 Evaluate side-chains 222 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain O residue 835 PHE Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1223 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN G 112 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17686 Z= 0.331 Angle : 0.698 11.128 25128 Z= 0.380 Chirality : 0.039 0.239 2863 Planarity : 0.005 0.054 2167 Dihedral : 30.119 178.887 4686 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.78 % Favored : 94.07 % Rotamer: Outliers : 4.53 % Allowed : 20.80 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1316 helix: 0.53 (0.19), residues: 773 sheet: -1.19 (0.66), residues: 66 loop : -1.31 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 777 HIS 0.008 0.001 HIS O 913 PHE 0.024 0.002 PHE O1063 TYR 0.049 0.002 TYR H 80 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9199 (mmm) cc_final: 0.8996 (tpt) REVERT: C 64 GLU cc_start: 0.8909 (tt0) cc_final: 0.8640 (pt0) REVERT: C 72 ASP cc_start: 0.8721 (m-30) cc_final: 0.8446 (m-30) REVERT: E 52 ARG cc_start: 0.9052 (mtp-110) cc_final: 0.8490 (ptm-80) REVERT: E 100 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (mt) REVERT: F 25 ASN cc_start: 0.6755 (m-40) cc_final: 0.6266 (m-40) REVERT: F 27 GLN cc_start: 0.8984 (pp30) cc_final: 0.8566 (pp30) REVERT: F 63 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8355 (mt-10) REVERT: F 80 THR cc_start: 0.9209 (m) cc_final: 0.8955 (p) REVERT: O 750 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5803 (mmt90) REVERT: O 835 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: O 1026 MET cc_start: 0.7161 (ptp) cc_final: 0.5283 (mmm) REVERT: O 1223 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8843 (mm-30) outliers start: 52 outliers final: 36 residues processed: 223 average time/residue: 0.3101 time to fit residues: 101.2966 Evaluate side-chains 219 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 835 PHE Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1223 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17686 Z= 0.217 Angle : 0.655 10.495 25128 Z= 0.357 Chirality : 0.037 0.267 2863 Planarity : 0.004 0.057 2167 Dihedral : 29.958 179.990 4686 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.02 % Favored : 94.83 % Rotamer: Outliers : 3.13 % Allowed : 21.93 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1316 helix: 0.69 (0.20), residues: 778 sheet: -1.08 (0.66), residues: 66 loop : -1.31 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 777 HIS 0.007 0.001 HIS O 913 PHE 0.023 0.002 PHE O1063 TYR 0.037 0.002 TYR H 80 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9121 (mmm) cc_final: 0.8839 (tpt) REVERT: C 64 GLU cc_start: 0.8896 (tt0) cc_final: 0.8621 (pt0) REVERT: C 72 ASP cc_start: 0.8738 (m-30) cc_final: 0.8457 (m-30) REVERT: D 39 TYR cc_start: 0.8058 (t80) cc_final: 0.7688 (t80) REVERT: D 105 LYS cc_start: 0.8773 (ptmm) cc_final: 0.8459 (pttm) REVERT: E 52 ARG cc_start: 0.8977 (mtp-110) cc_final: 0.8382 (ptm-80) REVERT: E 100 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8838 (mt) REVERT: F 25 ASN cc_start: 0.6434 (m-40) cc_final: 0.6066 (m-40) REVERT: F 27 GLN cc_start: 0.8938 (pp30) cc_final: 0.8603 (pp30) REVERT: F 63 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8342 (mt-10) REVERT: F 80 THR cc_start: 0.9144 (m) cc_final: 0.8914 (p) REVERT: O 750 ARG cc_start: 0.6935 (ptt-90) cc_final: 0.5808 (mmt90) REVERT: O 1223 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8861 (mm-30) outliers start: 36 outliers final: 28 residues processed: 221 average time/residue: 0.3005 time to fit residues: 98.4418 Evaluate side-chains 219 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 144 optimal weight: 0.0050 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 38 ASN G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17686 Z= 0.306 Angle : 0.692 11.484 25128 Z= 0.375 Chirality : 0.039 0.244 2863 Planarity : 0.005 0.056 2167 Dihedral : 30.088 178.365 4686 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.93 % Favored : 93.84 % Rotamer: Outliers : 3.22 % Allowed : 22.11 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1316 helix: 0.66 (0.19), residues: 777 sheet: -1.13 (0.66), residues: 66 loop : -1.33 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 777 HIS 0.008 0.001 HIS O 913 PHE 0.025 0.002 PHE O1063 TYR 0.042 0.002 TYR H 80 ARG 0.006 0.001 ARG C 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9168 (mmm) cc_final: 0.8882 (tpt) REVERT: C 64 GLU cc_start: 0.8905 (tt0) cc_final: 0.8637 (pt0) REVERT: C 72 ASP cc_start: 0.8794 (m-30) cc_final: 0.8505 (m-30) REVERT: E 52 ARG cc_start: 0.9015 (mtp-110) cc_final: 0.8470 (ptm-80) REVERT: E 100 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8916 (mt) REVERT: F 25 ASN cc_start: 0.6464 (m-40) cc_final: 0.6042 (m-40) REVERT: F 27 GLN cc_start: 0.8989 (pp30) cc_final: 0.8578 (pp30) REVERT: F 63 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8454 (mt-10) REVERT: F 80 THR cc_start: 0.9180 (m) cc_final: 0.8943 (p) REVERT: O 750 ARG cc_start: 0.7096 (ptt-90) cc_final: 0.5822 (mmt90) REVERT: O 1026 MET cc_start: 0.7236 (ptp) cc_final: 0.5320 (mmm) REVERT: O 1300 MET cc_start: 0.6961 (ttp) cc_final: 0.6681 (ptm) outliers start: 37 outliers final: 34 residues processed: 216 average time/residue: 0.2993 time to fit residues: 95.8734 Evaluate side-chains 222 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1083 TRP Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061860 restraints weight = 60657.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063433 restraints weight = 31880.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064431 restraints weight = 22328.174| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17686 Z= 0.279 Angle : 0.842 58.922 25128 Z= 0.478 Chirality : 0.040 0.775 2863 Planarity : 0.005 0.075 2167 Dihedral : 30.093 178.449 4686 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.70 % Favored : 94.00 % Rotamer: Outliers : 3.22 % Allowed : 22.02 % Favored : 74.76 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1316 helix: 0.68 (0.19), residues: 777 sheet: -1.13 (0.66), residues: 66 loop : -1.34 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 777 HIS 0.008 0.001 HIS O 913 PHE 0.025 0.002 PHE O1063 TYR 0.036 0.002 TYR H 80 ARG 0.005 0.000 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.41 seconds wall clock time: 59 minutes 46.40 seconds (3586.40 seconds total)