Starting phenix.real_space_refine on Sat Jun 28 18:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020.map" model { file = "/net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bfn_16020/06_2025/8bfn_16020_trim.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 20848 2.51 5 N 6120 2.21 5 O 6360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33400 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "F" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "G" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "H" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "I" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "J" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.65, per 1000 atoms: 0.59 Number of scatterers: 33400 At special positions: 0 Unit cell: (163.786, 177.725, 160.301, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 6360 8.00 N 6120 7.00 C 20848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 5.0 seconds 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7820 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 26 sheets defined 61.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.619A pdb=" N SER A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 6' Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 152 through 175 removed outlier: 8.341A pdb=" N THR A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.735A pdb=" N TYR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.916A pdb=" N PHE A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 283 removed outlier: 3.580A pdb=" N ALA A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 783 through 808 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.735A pdb=" N GLU A 814 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 835 removed outlier: 3.549A pdb=" N TYR A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.772A pdb=" N ASN A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 883 removed outlier: 3.648A pdb=" N GLU A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 947 through 955 Processing helix chain 'A' and resid 956 through 959 removed outlier: 3.706A pdb=" N ARG A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 985 through 1006 Processing helix chain 'A' and resid 1028 through 1042 removed outlier: 3.607A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.727A pdb=" N GLY B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.489A pdb=" N LYS B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 152 through 175 removed outlier: 8.774A pdb=" N THR B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.561A pdb=" N TYR B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.776A pdb=" N PHE B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.708A pdb=" N GLU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 283 Proline residue: B 264 - end of helix removed outlier: 3.705A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.944A pdb=" N GLU B 789 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 821 through 835 removed outlier: 3.535A pdb=" N TYR B 825 " --> pdb=" O ASP B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 851 Processing helix chain 'B' and resid 856 through 884 removed outlier: 3.767A pdb=" N VAL B 884 " --> pdb=" O THR B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 918 removed outlier: 3.606A pdb=" N ARG B 905 " --> pdb=" O HIS B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 944 Processing helix chain 'B' and resid 947 through 955 Processing helix chain 'B' and resid 956 through 959 Processing helix chain 'B' and resid 986 through 1006 Processing helix chain 'B' and resid 1028 through 1042 removed outlier: 3.568A pdb=" N ARG B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 Processing helix chain 'C' and resid 45 through 59 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.549A pdb=" N GLU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.882A pdb=" N LEU C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 4.038A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.879A pdb=" N HIS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'D' and resid 45 through 59 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 126 through 148 Processing helix chain 'D' and resid 158 through 170 Proline residue: D 163 - end of helix removed outlier: 3.792A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 4.028A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.753A pdb=" N ARG E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 Processing helix chain 'E' and resid 29 through 44 removed outlier: 4.091A pdb=" N LYS E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.923A pdb=" N ASP E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 144 Processing helix chain 'E' and resid 146 through 170 removed outlier: 3.680A pdb=" N ARG E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 220 Processing helix chain 'E' and resid 224 through 232 removed outlier: 5.435A pdb=" N ARG E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.758A pdb=" N GLN E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 273 through 280 removed outlier: 3.946A pdb=" N SER E 277 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 290 through 318 Processing helix chain 'E' and resid 321 through 339 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 398 through 406 removed outlier: 3.739A pdb=" N TRP E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 425 Processing helix chain 'E' and resid 429 through 437 Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.838A pdb=" N VAL E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 495 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N GLY F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.637A pdb=" N LEU F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 152 through 175 removed outlier: 7.808A pdb=" N THR F 165 " --> pdb=" O HIS F 161 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.605A pdb=" N TYR F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 208 removed outlier: 3.959A pdb=" N PHE F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 231 through 283 removed outlier: 3.868A pdb=" N ALA F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 783 through 807 Processing helix chain 'F' and resid 810 through 814 removed outlier: 3.787A pdb=" N GLU F 814 " --> pdb=" O ALA F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 820 No H-bonds generated for 'chain 'F' and resid 818 through 820' Processing helix chain 'F' and resid 821 through 835 Processing helix chain 'F' and resid 835 through 851 removed outlier: 3.506A pdb=" N ASN F 849 " --> pdb=" O LEU F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 882 removed outlier: 3.919A pdb=" N GLU F 879 " --> pdb=" O ASN F 875 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 918 removed outlier: 3.518A pdb=" N ARG F 905 " --> pdb=" O HIS F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 944 Processing helix chain 'F' and resid 947 through 955 Processing helix chain 'F' and resid 956 through 959 removed outlier: 3.697A pdb=" N ARG F 959 " --> pdb=" O PRO F 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 956 through 959' Processing helix chain 'F' and resid 985 through 1006 Processing helix chain 'F' and resid 1028 through 1042 removed outlier: 4.016A pdb=" N ARG F1034 " --> pdb=" O ALA F1030 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1060 removed outlier: 3.994A pdb=" N ASP F1060 " --> pdb=" O ARG F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1094 Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.802A pdb=" N GLY G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 6 through 11 removed outlier: 4.493A pdb=" N LYS G 10 " --> pdb=" O GLY G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 79 through 86 Processing helix chain 'G' and resid 152 through 175 removed outlier: 8.652A pdb=" N THR G 165 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 196 removed outlier: 3.545A pdb=" N PHE G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 210 removed outlier: 3.825A pdb=" N PHE G 202 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY G 210 " --> pdb=" O ASN G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 223 removed outlier: 3.634A pdb=" N GLU G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 283 Proline residue: G 264 - end of helix removed outlier: 3.701A pdb=" N TRP G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 808 removed outlier: 3.874A pdb=" N GLU G 789 " --> pdb=" O ARG G 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 807 " --> pdb=" O GLU G 803 " (cutoff:3.500A) Processing helix chain 'G' and resid 818 through 820 No H-bonds generated for 'chain 'G' and resid 818 through 820' Processing helix chain 'G' and resid 821 through 835 Processing helix chain 'G' and resid 835 through 851 Processing helix chain 'G' and resid 856 through 884 removed outlier: 3.635A pdb=" N VAL G 884 " --> pdb=" O THR G 880 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 918 Processing helix chain 'G' and resid 924 through 944 Processing helix chain 'G' and resid 947 through 955 Processing helix chain 'G' and resid 956 through 959 Processing helix chain 'G' and resid 986 through 1006 Processing helix chain 'G' and resid 1028 through 1042 removed outlier: 3.944A pdb=" N ARG G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1054 through 1061 Processing helix chain 'H' and resid 45 through 59 Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 126 through 146 Processing helix chain 'H' and resid 158 through 170 removed outlier: 3.800A pdb=" N LEU H 162 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Proline residue: H 163 - end of helix removed outlier: 3.580A pdb=" N ILE H 167 " --> pdb=" O PRO H 163 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 removed outlier: 3.501A pdb=" N HIS H 192 " --> pdb=" O GLN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 214 removed outlier: 3.888A pdb=" N HIS H 212 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 Processing helix chain 'I' and resid 45 through 59 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 76 through 85 Processing helix chain 'I' and resid 126 through 148 Processing helix chain 'I' and resid 158 through 170 Proline residue: I 163 - end of helix removed outlier: 3.942A pdb=" N TYR I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 192 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 215 through 234 removed outlier: 4.072A pdb=" N LEU I 219 " --> pdb=" O ASP I 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 19 removed outlier: 3.622A pdb=" N ARG J 8 " --> pdb=" O ASN J 4 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 27 Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.972A pdb=" N LYS J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.704A pdb=" N HIS J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 90 Processing helix chain 'J' and resid 104 through 118 removed outlier: 3.880A pdb=" N ASP J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 146 through 170 removed outlier: 3.587A pdb=" N ARG J 150 " --> pdb=" O ASN J 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 156 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG J 157 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 158 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 170 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 194 removed outlier: 3.550A pdb=" N ALA J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 182 " --> pdb=" O THR J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 198 through 220 removed outlier: 3.546A pdb=" N GLU J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 232 removed outlier: 3.657A pdb=" N VAL J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG J 230 " --> pdb=" O ASP J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 256 Processing helix chain 'J' and resid 258 through 272 Processing helix chain 'J' and resid 273 through 280 removed outlier: 3.884A pdb=" N SER J 277 " --> pdb=" O HIS J 273 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 290 Processing helix chain 'J' and resid 290 through 318 Processing helix chain 'J' and resid 321 through 339 Processing helix chain 'J' and resid 340 through 342 No H-bonds generated for 'chain 'J' and resid 340 through 342' Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 368 through 370 No H-bonds generated for 'chain 'J' and resid 368 through 370' Processing helix chain 'J' and resid 378 through 391 Processing helix chain 'J' and resid 398 through 406 removed outlier: 3.930A pdb=" N TRP J 402 " --> pdb=" O GLY J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 425 Processing helix chain 'J' and resid 429 through 437 Processing helix chain 'J' and resid 442 through 456 removed outlier: 3.502A pdb=" N PHE J 446 " --> pdb=" O ASP J 442 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL J 448 " --> pdb=" O GLU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.067A pdb=" N GLY A 28 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 21 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS A 30 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 19 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 32 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG A 17 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU A 15 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU A 115 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 17 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP A 23 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL A 107 " --> pdb=" O TRP A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1017 through 1021 removed outlier: 6.394A pdb=" N ILE A1018 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A1049 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A1020 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 40 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A1068 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 42 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ARG A1070 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.590A pdb=" N GLY B 28 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 21 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS B 30 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU B 19 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 32 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG B 17 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU B 15 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU B 115 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 17 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP B 23 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL B 107 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1017 through 1020 removed outlier: 6.590A pdb=" N ILE B1018 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B1049 " --> pdb=" O ILE B1018 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B1020 " --> pdb=" O ILE B1049 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 40 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1068 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 42 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG B1070 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 893 through 895 removed outlier: 4.120A pdb=" N ALA B 963 " --> pdb=" O ASP B 895 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 966 " --> pdb=" O ILE B 975 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.082A pdb=" N GLN D 123 " --> pdb=" O ARG E 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.693A pdb=" N ALA D 154 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'E' and resid 461 through 465 Processing sheet with id=AB5, first strand: chain 'F' and resid 26 through 32 removed outlier: 6.066A pdb=" N GLY F 28 " --> pdb=" O PHE F 21 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE F 21 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS F 30 " --> pdb=" O GLU F 19 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU F 19 " --> pdb=" O HIS F 30 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA F 32 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 17 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR F 113 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 18 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA F 111 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU F 20 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY F 109 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASN F 22 " --> pdb=" O VAL F 107 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL F 107 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 144 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 1017 through 1021 removed outlier: 6.553A pdb=" N ILE F1018 " --> pdb=" O VAL F1047 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE F1049 " --> pdb=" O ILE F1018 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F1020 " --> pdb=" O ILE F1049 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 39 " --> pdb=" O ALA F1046 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA F 40 " --> pdb=" O ILE F1066 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F1068 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 42 " --> pdb=" O VAL F1068 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ARG F1070 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 892 through 895 Processing sheet with id=AB8, first strand: chain 'G' and resid 26 through 33 removed outlier: 7.155A pdb=" N GLY G 28 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU G 15 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU G 115 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG G 17 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TRP G 23 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N VAL G 107 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 124 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1017 through 1020 removed outlier: 6.605A pdb=" N ILE G1018 " --> pdb=" O VAL G1047 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE G1049 " --> pdb=" O ILE G1018 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU G1020 " --> pdb=" O ILE G1049 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR G 39 " --> pdb=" O ALA G1046 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA G 40 " --> pdb=" O ILE G1066 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G1068 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 42 " --> pdb=" O VAL G1068 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ARG G1070 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER G1081 " --> pdb=" O ASN J 481 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 893 through 895 removed outlier: 4.040A pdb=" N ALA G 963 " --> pdb=" O ASP G 895 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL G 966 " --> pdb=" O ILE G 975 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 60 through 62 Processing sheet with id=AC3, first strand: chain 'H' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'I' and resid 60 through 62 Processing sheet with id=AC5, first strand: chain 'I' and resid 123 through 124 removed outlier: 6.058A pdb=" N GLN I 123 " --> pdb=" O ARG J 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC7, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AC8, first strand: chain 'J' and resid 461 through 465 1985 hydrogen bonds defined for protein. 5820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.90 Time building geometry restraints manager: 10.84 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: 9557 1.33 - 1.45: 5161 1.45 - 1.57: 19124 1.57 - 1.69: 16 1.69 - 1.81: 114 Bond restraints: 33972 Sorted by residual: bond pdb=" C5 ADP F1101 " pdb=" C6 ADP F1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C5 ADP A1101 " pdb=" C6 ADP A1101 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C5 ADP B1101 " pdb=" C6 ADP B1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C5 ADP G1101 " pdb=" C6 ADP G1101 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C5 ADP B1101 " pdb=" N7 ADP B1101 " ideal model delta sigma weight residual 1.350 1.474 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 33967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 45817 3.77 - 7.55: 114 7.55 - 11.32: 17 11.32 - 15.09: 4 15.09 - 18.86: 12 Bond angle restraints: 45964 Sorted by residual: angle pdb=" CA PRO D 198 " pdb=" N PRO D 198 " pdb=" CD PRO D 198 " ideal model delta sigma weight residual 112.00 101.73 10.27 1.40e+00 5.10e-01 5.38e+01 angle pdb=" O1A ADP G1101 " pdb=" PA ADP G1101 " pdb=" O2A ADP G1101 " ideal model delta sigma weight residual 119.90 101.04 18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" O1A ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sigma weight residual 119.90 101.07 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" O1A ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sigma weight residual 119.90 101.53 18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1A ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sigma weight residual 119.90 101.54 18.36 3.00e+00 1.11e-01 3.74e+01 ... (remaining 45959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 19579 33.17 - 66.33: 976 66.33 - 99.50: 104 99.50 - 132.66: 0 132.66 - 165.83: 5 Dihedral angle restraints: 20664 sinusoidal: 8614 harmonic: 12050 Sorted by residual: dihedral pdb=" C5' ADP F1101 " pdb=" O5' ADP F1101 " pdb=" PA ADP F1101 " pdb=" O2A ADP F1101 " ideal model delta sinusoidal sigma weight residual -60.00 105.83 -165.83 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1101 " pdb=" O3A ADP A1101 " pdb=" PB ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 142.55 157.45 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 20661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3453 0.030 - 0.059: 1118 0.059 - 0.089: 372 0.089 - 0.118: 187 0.118 - 0.148: 16 Chirality restraints: 5146 Sorted by residual: chirality pdb=" CG LEU F 224 " pdb=" CB LEU F 224 " pdb=" CD1 LEU F 224 " pdb=" CD2 LEU F 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE E 366 " pdb=" N ILE E 366 " pdb=" C ILE E 366 " pdb=" CB ILE E 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE J 366 " pdb=" N ILE J 366 " pdb=" C ILE J 366 " pdb=" CB ILE J 366 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 5143 not shown) Planarity restraints: 6034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 197 " -0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO D 198 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 887 " 0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO F 888 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 888 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 888 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 887 " -0.057 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO A 888 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " -0.047 5.00e-02 4.00e+02 ... (remaining 6031 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 355 2.52 - 3.11: 28284 3.11 - 3.71: 54376 3.71 - 4.30: 74232 4.30 - 4.90: 122741 Nonbonded interactions: 279988 Sorted by model distance: nonbonded pdb=" OG SER F 971 " pdb=" OD1 ASN F 973 " model vdw 1.921 3.040 nonbonded pdb=" OG SER A 971 " pdb=" OD1 ASN A 973 " model vdw 1.921 3.040 nonbonded pdb=" O ASN B 22 " pdb=" OG1 THR B 108 " model vdw 1.934 3.040 nonbonded pdb=" O LEU B1058 " pdb=" OG1 THR B1062 " model vdw 1.945 3.040 nonbonded pdb=" O SER A 852 " pdb=" OG1 THR A 857 " model vdw 1.949 3.040 ... (remaining 279983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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: 3.850 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: 0.040 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 77.450 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 33972 Z= 0.219 Angle : 0.668 18.863 45964 Z= 0.324 Chirality : 0.037 0.148 5146 Planarity : 0.004 0.095 6034 Dihedral : 19.102 165.826 12844 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 45.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 0.48 % Allowed : 33.16 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 4136 helix: 1.96 (0.11), residues: 2346 sheet: -0.91 (0.23), residues: 520 loop : -1.44 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 156 HIS 0.007 0.001 HIS G1029 PHE 0.017 0.001 PHE G 194 TYR 0.025 0.001 TYR A 891 ARG 0.009 0.000 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.17853 ( 1985) hydrogen bonds : angle 6.49648 ( 5820) covalent geometry : bond 0.00471 (33972) covalent geometry : angle 0.66814 (45964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 818 time to evaluate : 3.823 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: B 171 MET cc_start: 0.6401 (ptt) cc_final: 0.6042 (ptt) REVERT: F 801 MET cc_start: 0.7293 (mtt) cc_final: 0.6870 (mmt) REVERT: G 34 ILE cc_start: 0.8630 (mp) cc_final: 0.8380 (mp) REVERT: G 172 GLU cc_start: 0.6299 (tt0) cc_final: 0.4556 (tp30) REVERT: G 234 ARG cc_start: 0.3446 (mmm-85) cc_final: 0.2982 (mtt-85) REVERT: G 801 MET cc_start: 0.7427 (ttm) cc_final: 0.7195 (ttt) REVERT: J 211 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7580 (ttm110) REVERT: J 263 MET cc_start: 0.7795 (mtt) cc_final: 0.7258 (mtm) REVERT: J 454 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7199 (ttt180) outliers start: 17 outliers final: 12 residues processed: 829 average time/residue: 0.4847 time to fit residues: 630.8927 Evaluate side-chains 800 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 788 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 321 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 372 optimal weight: 0.8980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 830 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G 213 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS G1073 GLN H 218 ASN J 138 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130526 restraints weight = 52094.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129503 restraints weight = 26887.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129988 restraints weight = 25447.711| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33972 Z= 0.192 Angle : 0.735 15.030 45964 Z= 0.365 Chirality : 0.044 0.203 5146 Planarity : 0.005 0.059 6034 Dihedral : 7.568 153.404 4661 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.56 % Favored : 94.22 % Rotamer: Outliers : 5.34 % Allowed : 26.84 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 4136 helix: 1.73 (0.10), residues: 2400 sheet: -0.76 (0.23), residues: 480 loop : -1.47 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 128 HIS 0.012 0.001 HIS B1029 PHE 0.021 0.002 PHE G 194 TYR 0.023 0.002 TYR A 891 ARG 0.007 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 1985) hydrogen bonds : angle 4.86280 ( 5820) covalent geometry : bond 0.00440 (33972) covalent geometry : angle 0.73485 (45964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 911 time to evaluate : 3.497 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: A 801 MET cc_start: 0.7016 (mtt) cc_final: 0.6746 (mtt) REVERT: A 1054 GLU cc_start: 0.8044 (mp0) cc_final: 0.7392 (mt-10) REVERT: B 172 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6316 (tm-30) REVERT: B 186 GLN cc_start: 0.7840 (tt0) cc_final: 0.7593 (pt0) REVERT: B 219 GLU cc_start: 0.8033 (mp0) cc_final: 0.7404 (tt0) REVERT: B 234 ARG cc_start: 0.3359 (mmm-85) cc_final: 0.2652 (mtp85) REVERT: B 253 GLU cc_start: 0.5448 (mm-30) cc_final: 0.4606 (mm-30) REVERT: B 792 ARG cc_start: 0.6923 (mtm110) cc_final: 0.6671 (ptt-90) REVERT: B 978 ARG cc_start: 0.1843 (OUTLIER) cc_final: 0.0494 (ptm160) REVERT: B 1076 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6492 (p0) REVERT: C 46 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 76 HIS cc_start: 0.8030 (m90) cc_final: 0.7466 (m90) REVERT: C 146 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6349 (tm-30) REVERT: D 54 GLU cc_start: 0.7309 (tp30) cc_final: 0.7067 (mm-30) REVERT: E 80 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6952 (tp-100) REVERT: E 442 ASP cc_start: 0.7368 (m-30) cc_final: 0.7146 (t70) REVERT: E 443 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7690 (pt) REVERT: E 452 MET cc_start: 0.7454 (mmt) cc_final: 0.7157 (mmt) REVERT: E 461 ILE cc_start: 0.7590 (pt) cc_final: 0.7323 (mp) REVERT: E 494 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5667 (t70) REVERT: F 185 LYS cc_start: 0.8490 (tppt) cc_final: 0.8238 (mtmm) REVERT: F 1054 GLU cc_start: 0.7902 (mp0) cc_final: 0.7466 (mt-10) REVERT: G 34 ILE cc_start: 0.8760 (mp) cc_final: 0.8467 (mp) REVERT: G 144 LEU cc_start: 0.7129 (mt) cc_final: 0.6913 (mt) REVERT: G 155 HIS cc_start: 0.7543 (t-170) cc_final: 0.7286 (t-170) REVERT: G 172 GLU cc_start: 0.6250 (tt0) cc_final: 0.4629 (tp30) REVERT: G 234 ARG cc_start: 0.3681 (mmm-85) cc_final: 0.3361 (mtp85) REVERT: G 248 ILE cc_start: 0.7587 (mt) cc_final: 0.7224 (mp) REVERT: G 270 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: G 789 GLU cc_start: 0.6846 (tt0) cc_final: 0.6615 (tt0) REVERT: G 871 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6659 (tm-30) REVERT: G 978 ARG cc_start: 0.1846 (OUTLIER) cc_final: 0.0482 (ptm160) REVERT: G 1076 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6740 (p0) REVERT: I 215 ASP cc_start: 0.7356 (p0) cc_final: 0.7086 (p0) REVERT: I 227 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7536 (ttm110) REVERT: J 96 GLU cc_start: 0.6729 (tp30) cc_final: 0.6451 (tp30) REVERT: J 161 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5800 (mt) REVERT: J 211 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7682 (ttm110) REVERT: J 263 MET cc_start: 0.7806 (mtt) cc_final: 0.7471 (mtm) REVERT: J 399 ASP cc_start: 0.7529 (t0) cc_final: 0.7255 (t0) REVERT: J 409 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6549 (p0) REVERT: J 452 MET cc_start: 0.7346 (mmt) cc_final: 0.6983 (mmt) outliers start: 190 outliers final: 99 residues processed: 1030 average time/residue: 0.4911 time to fit residues: 796.8374 Evaluate side-chains 914 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 805 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1002 SER Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1029 HIS Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain G residue 1077 MET Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 409 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 89 optimal weight: 5.9990 chunk 52 optimal weight: 0.0040 chunk 5 optimal weight: 0.1980 chunk 298 optimal weight: 0.7980 chunk 335 optimal weight: 0.3980 chunk 281 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 275 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 830 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1073 GLN H 53 GLN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128401 restraints weight = 52987.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127268 restraints weight = 28136.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127938 restraints weight = 26006.663| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33972 Z= 0.148 Angle : 0.672 14.026 45964 Z= 0.331 Chirality : 0.042 0.350 5146 Planarity : 0.004 0.054 6034 Dihedral : 7.276 156.346 4646 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 4.83 % Allowed : 27.32 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 4136 helix: 1.71 (0.10), residues: 2388 sheet: -0.84 (0.23), residues: 468 loop : -1.38 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 128 HIS 0.020 0.001 HIS G1029 PHE 0.022 0.002 PHE G 194 TYR 0.032 0.002 TYR B 891 ARG 0.008 0.001 ARG J 134 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1985) hydrogen bonds : angle 4.64335 ( 5820) covalent geometry : bond 0.00322 (33972) covalent geometry : angle 0.67208 (45964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 905 time to evaluate : 3.890 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: A 67 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6273 (m110) REVERT: A 1054 GLU cc_start: 0.8008 (mp0) cc_final: 0.7451 (mt-10) REVERT: B 172 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6440 (tm-30) REVERT: B 186 GLN cc_start: 0.7898 (tt0) cc_final: 0.7639 (pt0) REVERT: B 219 GLU cc_start: 0.8054 (mp0) cc_final: 0.7838 (pm20) REVERT: B 234 ARG cc_start: 0.2977 (mmm-85) cc_final: 0.2732 (mtp85) REVERT: B 248 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7213 (mt) REVERT: B 253 GLU cc_start: 0.5463 (mm-30) cc_final: 0.5229 (mm-30) REVERT: B 269 TRP cc_start: 0.7408 (t-100) cc_final: 0.6996 (t-100) REVERT: B 270 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: B 273 GLN cc_start: 0.6941 (mt0) cc_final: 0.6713 (mt0) REVERT: B 792 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6730 (ptt-90) REVERT: B 796 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 800 ARG cc_start: 0.7315 (mmp-170) cc_final: 0.6759 (mmm160) REVERT: B 978 ARG cc_start: 0.1629 (OUTLIER) cc_final: 0.0571 (ptm160) REVERT: B 1003 TYR cc_start: 0.7507 (t80) cc_final: 0.7036 (t80) REVERT: B 1062 THR cc_start: 0.7682 (p) cc_final: 0.7429 (p) REVERT: C 45 LEU cc_start: 0.8700 (mp) cc_final: 0.8171 (tp) REVERT: C 46 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 146 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6808 (tm-30) REVERT: C 159 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: D 54 GLU cc_start: 0.7358 (tp30) cc_final: 0.7109 (mm-30) REVERT: D 215 ASP cc_start: 0.7108 (p0) cc_final: 0.6684 (p0) REVERT: E 96 GLU cc_start: 0.6767 (tp30) cc_final: 0.6484 (tp30) REVERT: E 125 THR cc_start: 0.8991 (p) cc_final: 0.8790 (p) REVERT: E 134 ARG cc_start: 0.6904 (mtm180) cc_final: 0.6424 (mtm180) REVERT: E 227 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7907 (mm) REVERT: E 409 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6153 (p0) REVERT: E 442 ASP cc_start: 0.7296 (m-30) cc_final: 0.7050 (t70) REVERT: E 452 MET cc_start: 0.7564 (mmt) cc_final: 0.7223 (mmt) REVERT: E 461 ILE cc_start: 0.7829 (pt) cc_final: 0.7457 (mp) REVERT: E 494 ASP cc_start: 0.6063 (OUTLIER) cc_final: 0.5684 (t70) REVERT: F 115 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7126 (mt-10) REVERT: F 185 LYS cc_start: 0.8528 (tppt) cc_final: 0.8269 (mtmm) REVERT: F 192 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7660 (mtt180) REVERT: F 234 ARG cc_start: 0.8050 (tpt170) cc_final: 0.7845 (tpt170) REVERT: F 929 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8319 (mtmm) REVERT: F 976 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: F 1054 GLU cc_start: 0.7957 (mp0) cc_final: 0.7535 (mt-10) REVERT: G 34 ILE cc_start: 0.8749 (mp) cc_final: 0.8476 (mp) REVERT: G 155 HIS cc_start: 0.7539 (t-170) cc_final: 0.7331 (t-170) REVERT: G 172 GLU cc_start: 0.6102 (tt0) cc_final: 0.4691 (tp30) REVERT: G 219 GLU cc_start: 0.7968 (pm20) cc_final: 0.7479 (tt0) REVERT: G 234 ARG cc_start: 0.3763 (mmm-85) cc_final: 0.2979 (mtp85) REVERT: G 248 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7386 (mp) REVERT: G 253 GLU cc_start: 0.5385 (mm-30) cc_final: 0.4702 (mm-30) REVERT: G 270 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: G 789 GLU cc_start: 0.6687 (tt0) cc_final: 0.6448 (tt0) REVERT: G 871 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6499 (tm-30) REVERT: H 76 HIS cc_start: 0.7852 (m90) cc_final: 0.7392 (m90) REVERT: I 54 GLU cc_start: 0.7238 (tp30) cc_final: 0.6949 (tp30) REVERT: I 100 LEU cc_start: 0.8869 (mt) cc_final: 0.8642 (mt) REVERT: I 215 ASP cc_start: 0.7291 (p0) cc_final: 0.6903 (p0) REVERT: J 6 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7435 (mtm110) REVERT: J 96 GLU cc_start: 0.6808 (tp30) cc_final: 0.6601 (tp30) REVERT: J 161 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5717 (mt) REVERT: J 211 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7605 (ttm110) REVERT: J 263 MET cc_start: 0.7718 (mtt) cc_final: 0.7386 (mtm) REVERT: J 294 ARG cc_start: 0.7683 (ptp-110) cc_final: 0.7228 (ptp-170) REVERT: J 399 ASP cc_start: 0.7538 (t0) cc_final: 0.7206 (t0) REVERT: J 409 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6488 (p0) REVERT: J 418 LEU cc_start: 0.7530 (pp) cc_final: 0.7293 (pp) REVERT: J 452 MET cc_start: 0.7424 (mmt) cc_final: 0.7199 (mmt) REVERT: J 467 PHE cc_start: 0.6674 (m-80) cc_final: 0.6445 (m-80) outliers start: 172 outliers final: 85 residues processed: 1007 average time/residue: 0.4702 time to fit residues: 745.0126 Evaluate side-chains 937 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 838 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1029 HIS Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 881 MET Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1029 HIS Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1077 MET Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 161 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 335 optimal weight: 0.7980 chunk 328 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 191 optimal weight: 0.0000 chunk 68 optimal weight: 10.0000 chunk 315 optimal weight: 0.2980 chunk 222 optimal weight: 2.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 275 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 396 GLN F 67 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G1029 HIS J 396 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129215 restraints weight = 52966.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128502 restraints weight = 27478.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129092 restraints weight = 23840.108| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33972 Z= 0.134 Angle : 0.657 12.913 45964 Z= 0.322 Chirality : 0.041 0.226 5146 Planarity : 0.004 0.055 6034 Dihedral : 7.047 159.688 4642 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 4.47 % Allowed : 28.13 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 4136 helix: 1.75 (0.10), residues: 2382 sheet: -0.81 (0.23), residues: 468 loop : -1.28 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 128 HIS 0.021 0.001 HIS B1029 PHE 0.023 0.001 PHE A 221 TYR 0.024 0.002 TYR A 891 ARG 0.011 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1985) hydrogen bonds : angle 4.48843 ( 5820) covalent geometry : bond 0.00294 (33972) covalent geometry : angle 0.65747 (45964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 915 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6336 (m110) REVERT: A 976 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: A 1054 GLU cc_start: 0.7928 (mp0) cc_final: 0.7721 (mt-10) REVERT: A 1092 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6298 (tmm-80) REVERT: B 57 MET cc_start: 0.7691 (mmm) cc_final: 0.7120 (mmm) REVERT: B 172 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6429 (tm-30) REVERT: B 186 GLN cc_start: 0.7950 (tt0) cc_final: 0.7679 (pt0) REVERT: B 269 TRP cc_start: 0.7399 (t-100) cc_final: 0.6948 (t-100) REVERT: B 270 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: B 273 GLN cc_start: 0.6963 (mt0) cc_final: 0.6748 (mt0) REVERT: B 792 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6791 (ptt-90) REVERT: B 796 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 800 ARG cc_start: 0.7324 (mmp-170) cc_final: 0.6744 (mmm160) REVERT: B 1076 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.6133 (p0) REVERT: C 45 LEU cc_start: 0.8742 (mp) cc_final: 0.8246 (tp) REVERT: C 146 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 159 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: D 178 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7301 (mp0) REVERT: D 215 ASP cc_start: 0.7126 (p0) cc_final: 0.6692 (p0) REVERT: E 96 GLU cc_start: 0.6768 (tp30) cc_final: 0.6559 (tp30) REVERT: E 125 THR cc_start: 0.8980 (p) cc_final: 0.8742 (p) REVERT: E 134 ARG cc_start: 0.6471 (mtm180) cc_final: 0.6105 (mtm180) REVERT: E 196 ARG cc_start: 0.7594 (tmt-80) cc_final: 0.7348 (tmt-80) REVERT: E 227 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7628 (mm) REVERT: E 294 ARG cc_start: 0.7626 (ptp-110) cc_final: 0.6980 (mtm180) REVERT: E 409 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6105 (p0) REVERT: E 452 MET cc_start: 0.7621 (mmt) cc_final: 0.6793 (mtp) REVERT: E 461 ILE cc_start: 0.7779 (pt) cc_final: 0.7478 (mp) REVERT: E 481 ASN cc_start: 0.7848 (t0) cc_final: 0.7395 (t0) REVERT: E 494 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5539 (t0) REVERT: F 67 ASN cc_start: 0.7010 (OUTLIER) cc_final: 0.6789 (m110) REVERT: F 234 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7772 (tpt170) REVERT: F 794 ASN cc_start: 0.8422 (t0) cc_final: 0.8097 (t0) REVERT: F 921 ASP cc_start: 0.7703 (t0) cc_final: 0.7320 (t0) REVERT: F 929 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8261 (mtmm) REVERT: F 1054 GLU cc_start: 0.7962 (mp0) cc_final: 0.7683 (mt-10) REVERT: G 34 ILE cc_start: 0.8733 (mp) cc_final: 0.8486 (mp) REVERT: G 144 LEU cc_start: 0.6777 (mt) cc_final: 0.6311 (pp) REVERT: G 155 HIS cc_start: 0.7466 (t-170) cc_final: 0.7238 (t-170) REVERT: G 172 GLU cc_start: 0.6327 (tt0) cc_final: 0.4816 (tp30) REVERT: G 219 GLU cc_start: 0.7936 (pm20) cc_final: 0.7424 (tt0) REVERT: G 237 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7391 (mm-30) REVERT: G 270 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: G 275 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6938 (tp40) REVERT: G 789 GLU cc_start: 0.6748 (tt0) cc_final: 0.6502 (tt0) REVERT: G 819 LEU cc_start: 0.6662 (pt) cc_final: 0.5717 (mm) REVERT: G 871 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6449 (tm-30) REVERT: G 893 ARG cc_start: 0.6706 (ptt180) cc_final: 0.6298 (mtp-110) REVERT: G 978 ARG cc_start: 0.1473 (OUTLIER) cc_final: 0.0482 (ptm160) REVERT: G 1076 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.6090 (p0) REVERT: H 45 LEU cc_start: 0.8717 (mp) cc_final: 0.8153 (tp) REVERT: I 54 GLU cc_start: 0.7209 (tp30) cc_final: 0.6934 (tp30) REVERT: I 101 TYR cc_start: 0.9018 (p90) cc_final: 0.8691 (p90) REVERT: I 215 ASP cc_start: 0.7341 (p0) cc_final: 0.7005 (p0) REVERT: J 6 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7318 (mtm110) REVERT: J 161 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5759 (mt) REVERT: J 211 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7552 (ttm110) REVERT: J 263 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7448 (mtm) REVERT: J 294 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.6839 (mtm180) REVERT: J 399 ASP cc_start: 0.7696 (t0) cc_final: 0.7398 (t0) REVERT: J 409 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6310 (p0) REVERT: J 452 MET cc_start: 0.7683 (mmt) cc_final: 0.6736 (mtp) outliers start: 159 outliers final: 98 residues processed: 1009 average time/residue: 0.4915 time to fit residues: 787.6795 Evaluate side-chains 945 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 829 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1077 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 275 GLN Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 802 SER Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 918 ARG Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain G residue 1077 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 349 optimal weight: 0.4980 chunk 268 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 376 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 HIS ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G 927 HIS G1029 HIS J 396 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126619 restraints weight = 53098.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125166 restraints weight = 29380.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125875 restraints weight = 26972.253| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33972 Z= 0.196 Angle : 0.692 12.546 45964 Z= 0.343 Chirality : 0.043 0.193 5146 Planarity : 0.005 0.062 6034 Dihedral : 7.107 156.811 4640 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 5.82 % Allowed : 28.58 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4136 helix: 1.53 (0.10), residues: 2412 sheet: -0.80 (0.23), residues: 464 loop : -1.44 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 128 HIS 0.006 0.001 HIS G1029 PHE 0.017 0.002 PHE A 221 TYR 0.026 0.002 TYR F 891 ARG 0.008 0.001 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 1985) hydrogen bonds : angle 4.59180 ( 5820) covalent geometry : bond 0.00455 (33972) covalent geometry : angle 0.69234 (45964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 853 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 976 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6527 (tp30) REVERT: A 1054 GLU cc_start: 0.7984 (mp0) cc_final: 0.7717 (mt-10) REVERT: B 31 GLN cc_start: 0.6121 (pt0) cc_final: 0.5794 (pt0) REVERT: B 171 MET cc_start: 0.6299 (ptt) cc_final: 0.6052 (ptt) REVERT: B 219 GLU cc_start: 0.7958 (pm20) cc_final: 0.7428 (tt0) REVERT: B 269 TRP cc_start: 0.7493 (t-100) cc_final: 0.7172 (t-100) REVERT: B 270 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: B 792 ARG cc_start: 0.6975 (mtm110) cc_final: 0.6751 (ptt-90) REVERT: B 796 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 800 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.6827 (mmm160) REVERT: B 819 LEU cc_start: 0.6625 (pt) cc_final: 0.5760 (mm) REVERT: B 978 ARG cc_start: 0.1332 (OUTLIER) cc_final: 0.0392 (ptm160) REVERT: B 1076 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6274 (p0) REVERT: C 45 LEU cc_start: 0.8735 (mp) cc_final: 0.8263 (tp) REVERT: C 146 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6909 (tm-30) REVERT: D 215 ASP cc_start: 0.7273 (p0) cc_final: 0.6864 (p0) REVERT: E 96 GLU cc_start: 0.6709 (tp30) cc_final: 0.6436 (tp30) REVERT: E 134 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6315 (mtm180) REVERT: E 163 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7062 (ptp-110) REVERT: E 227 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7765 (mm) REVERT: E 294 ARG cc_start: 0.7741 (ptp-110) cc_final: 0.7280 (ptp-170) REVERT: E 376 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: E 409 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6106 (p0) REVERT: E 452 MET cc_start: 0.7408 (mmt) cc_final: 0.6693 (mpp) REVERT: E 494 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5665 (t70) REVERT: F 56 LEU cc_start: 0.9004 (tt) cc_final: 0.8617 (tt) REVERT: F 234 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7857 (tpt170) REVERT: F 921 ASP cc_start: 0.7919 (t0) cc_final: 0.7560 (t0) REVERT: F 929 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: F 976 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6473 (tp30) REVERT: F 1054 GLU cc_start: 0.8015 (mp0) cc_final: 0.7587 (mt-10) REVERT: G 34 ILE cc_start: 0.8757 (mp) cc_final: 0.8492 (mp) REVERT: G 144 LEU cc_start: 0.6693 (mt) cc_final: 0.6349 (pp) REVERT: G 155 HIS cc_start: 0.7509 (t-170) cc_final: 0.7240 (t-170) REVERT: G 172 GLU cc_start: 0.6565 (tt0) cc_final: 0.4812 (tp30) REVERT: G 219 GLU cc_start: 0.7967 (pm20) cc_final: 0.7528 (tt0) REVERT: G 270 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: G 819 LEU cc_start: 0.6417 (pt) cc_final: 0.5514 (mm) REVERT: G 893 ARG cc_start: 0.6715 (ptt180) cc_final: 0.6225 (mtp-110) REVERT: G 967 MET cc_start: 0.5780 (mtp) cc_final: 0.5525 (mtp) REVERT: G 978 ARG cc_start: 0.1381 (OUTLIER) cc_final: 0.0449 (ptm160) REVERT: G 1076 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6341 (p0) REVERT: H 45 LEU cc_start: 0.8755 (mp) cc_final: 0.8248 (tp) REVERT: H 175 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7201 (tm-30) REVERT: I 178 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7266 (mp0) REVERT: I 215 ASP cc_start: 0.7452 (p0) cc_final: 0.7116 (p0) REVERT: I 227 ARG cc_start: 0.7472 (mtp85) cc_final: 0.6979 (mmm160) REVERT: J 201 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7564 (ttp80) REVERT: J 263 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7648 (mtm) REVERT: J 409 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6232 (p0) REVERT: J 452 MET cc_start: 0.7527 (mmt) cc_final: 0.6638 (mtp) outliers start: 207 outliers final: 132 residues processed: 983 average time/residue: 0.4800 time to fit residues: 748.0652 Evaluate side-chains 958 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 810 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 802 SER Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 812 LEU Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 978 ARG Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 ARG Chi-restraints excluded: chain J residue 494 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 254 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 chunk 342 optimal weight: 0.3980 chunk 236 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 11 ASN J 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127655 restraints weight = 52988.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126316 restraints weight = 28838.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127025 restraints weight = 26379.890| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33972 Z= 0.159 Angle : 0.677 12.173 45964 Z= 0.334 Chirality : 0.042 0.177 5146 Planarity : 0.004 0.066 6034 Dihedral : 6.983 158.159 4640 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 5.12 % Allowed : 29.20 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4136 helix: 1.54 (0.10), residues: 2410 sheet: -0.96 (0.23), residues: 492 loop : -1.43 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 128 HIS 0.008 0.001 HIS B1029 PHE 0.016 0.002 PHE F 886 TYR 0.025 0.002 TYR A 891 ARG 0.008 0.001 ARG A1091 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 1985) hydrogen bonds : angle 4.53938 ( 5820) covalent geometry : bond 0.00364 (33972) covalent geometry : angle 0.67713 (45964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 887 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 THR cc_start: 0.7685 (m) cc_final: 0.7455 (p) REVERT: A 976 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: A 1054 GLU cc_start: 0.7973 (mp0) cc_final: 0.7761 (mt-10) REVERT: B 169 ARG cc_start: 0.5875 (ttp-110) cc_final: 0.5666 (tmm160) REVERT: B 219 GLU cc_start: 0.8012 (pm20) cc_final: 0.7476 (tt0) REVERT: B 800 ARG cc_start: 0.7434 (mmp-170) cc_final: 0.6844 (mmm160) REVERT: B 819 LEU cc_start: 0.6870 (pt) cc_final: 0.5975 (mm) REVERT: B 931 LEU cc_start: 0.8444 (mm) cc_final: 0.8118 (mm) REVERT: B 961 GLU cc_start: 0.7338 (mp0) cc_final: 0.6973 (mp0) REVERT: B 1076 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6303 (p0) REVERT: C 45 LEU cc_start: 0.8732 (mp) cc_final: 0.8233 (tp) REVERT: C 146 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6970 (tm-30) REVERT: D 103 LYS cc_start: 0.8715 (ptpp) cc_final: 0.8467 (ptpp) REVERT: D 215 ASP cc_start: 0.7327 (p0) cc_final: 0.6880 (p0) REVERT: E 134 ARG cc_start: 0.6487 (mtm180) cc_final: 0.6241 (mtm180) REVERT: E 227 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7717 (mm) REVERT: E 294 ARG cc_start: 0.7744 (ptp-110) cc_final: 0.7310 (ptp-170) REVERT: E 409 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6058 (p0) REVERT: E 452 MET cc_start: 0.7690 (mmt) cc_final: 0.6908 (mtp) REVERT: E 494 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5554 (t0) REVERT: F 56 LEU cc_start: 0.9009 (tt) cc_final: 0.8641 (tt) REVERT: F 234 ARG cc_start: 0.8049 (tpt170) cc_final: 0.7840 (tpt170) REVERT: F 921 ASP cc_start: 0.7917 (t0) cc_final: 0.7647 (t0) REVERT: F 929 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: F 976 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6428 (tp30) REVERT: F 1054 GLU cc_start: 0.7981 (mp0) cc_final: 0.7581 (mt-10) REVERT: G 34 ILE cc_start: 0.8752 (mp) cc_final: 0.8480 (mp) REVERT: G 155 HIS cc_start: 0.7531 (t-170) cc_final: 0.7253 (t-170) REVERT: G 219 GLU cc_start: 0.7981 (pm20) cc_final: 0.7459 (tt0) REVERT: G 237 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7365 (mm-30) REVERT: G 819 LEU cc_start: 0.6442 (pt) cc_final: 0.5518 (mm) REVERT: G 871 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6504 (tm-30) REVERT: G 893 ARG cc_start: 0.6696 (ptt180) cc_final: 0.6247 (mtp-110) REVERT: G 960 LEU cc_start: 0.7349 (pt) cc_final: 0.6582 (pt) REVERT: G 1076 ASN cc_start: 0.6711 (OUTLIER) cc_final: 0.6433 (p0) REVERT: H 45 LEU cc_start: 0.8741 (mp) cc_final: 0.8235 (tp) REVERT: H 70 TYR cc_start: 0.8385 (t80) cc_final: 0.8123 (t80) REVERT: H 175 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 179 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: H 233 GLN cc_start: 0.7076 (pp30) cc_final: 0.6772 (pp30) REVERT: I 178 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7262 (mp0) REVERT: I 215 ASP cc_start: 0.7436 (p0) cc_final: 0.7120 (p0) REVERT: J 200 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8171 (mmp80) REVERT: J 201 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7516 (ttt90) REVERT: J 294 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7406 (ptp-170) REVERT: J 304 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: J 409 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6292 (p0) REVERT: J 452 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6957 (mtp) outliers start: 182 outliers final: 123 residues processed: 993 average time/residue: 0.4607 time to fit residues: 727.5520 Evaluate side-chains 973 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 838 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 331 optimal weight: 0.4980 chunk 202 optimal weight: 0.4980 chunk 395 optimal weight: 1.9990 chunk 335 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 283 optimal weight: 0.3980 chunk 322 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 354 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 160 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS J 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129092 restraints weight = 52858.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128738 restraints weight = 27764.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129206 restraints weight = 23451.739| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33972 Z= 0.137 Angle : 0.671 11.555 45964 Z= 0.332 Chirality : 0.041 0.189 5146 Planarity : 0.004 0.067 6034 Dihedral : 6.809 161.446 4640 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 4.64 % Allowed : 29.71 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 4136 helix: 1.63 (0.11), residues: 2398 sheet: -0.95 (0.23), residues: 492 loop : -1.40 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 128 HIS 0.007 0.001 HIS B1029 PHE 0.018 0.001 PHE F 886 TYR 0.025 0.002 TYR G 187 ARG 0.012 0.000 ARG G 192 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1985) hydrogen bonds : angle 4.47352 ( 5820) covalent geometry : bond 0.00303 (33972) covalent geometry : angle 0.67093 (45964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 896 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 976 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6492 (tp30) REVERT: A 1054 GLU cc_start: 0.7949 (mp0) cc_final: 0.7739 (mt-10) REVERT: B 17 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7912 (tpp80) REVERT: B 186 GLN cc_start: 0.7616 (tt0) cc_final: 0.7370 (pt0) REVERT: B 219 GLU cc_start: 0.7953 (pm20) cc_final: 0.7400 (tt0) REVERT: B 237 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7224 (mm-30) REVERT: B 256 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6636 (ptm160) REVERT: B 800 ARG cc_start: 0.7523 (mmp-170) cc_final: 0.6946 (mmm160) REVERT: B 961 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: B 1076 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6355 (p0) REVERT: C 45 LEU cc_start: 0.8712 (mp) cc_final: 0.8211 (tp) REVERT: C 121 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7367 (mtm-85) REVERT: C 146 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 233 GLN cc_start: 0.7086 (pp30) cc_final: 0.6575 (pp30) REVERT: D 103 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8383 (ptpp) REVERT: D 215 ASP cc_start: 0.7305 (p0) cc_final: 0.6841 (p0) REVERT: E 134 ARG cc_start: 0.6651 (mtm180) cc_final: 0.6381 (mtm180) REVERT: E 163 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7099 (mtm110) REVERT: E 227 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7778 (mm) REVERT: E 294 ARG cc_start: 0.7674 (ptp-110) cc_final: 0.7287 (ptp-170) REVERT: E 304 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: E 409 ASP cc_start: 0.6397 (OUTLIER) cc_final: 0.6105 (p0) REVERT: E 452 MET cc_start: 0.7694 (mmt) cc_final: 0.7037 (mtp) REVERT: E 494 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.5568 (t0) REVERT: F 56 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8644 (tt) REVERT: F 921 ASP cc_start: 0.7927 (t0) cc_final: 0.7714 (t0) REVERT: F 929 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: F 976 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: F 1054 GLU cc_start: 0.8024 (mp0) cc_final: 0.7770 (mt-10) REVERT: G 34 ILE cc_start: 0.8746 (mp) cc_final: 0.8505 (mp) REVERT: G 219 GLU cc_start: 0.7894 (pm20) cc_final: 0.7439 (tt0) REVERT: G 237 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7366 (mm-30) REVERT: G 253 GLU cc_start: 0.5604 (mm-30) cc_final: 0.4757 (mm-30) REVERT: G 270 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: G 802 SER cc_start: 0.7740 (m) cc_final: 0.7522 (p) REVERT: G 819 LEU cc_start: 0.6246 (pt) cc_final: 0.5431 (mm) REVERT: G 871 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6280 (tm-30) REVERT: G 893 ARG cc_start: 0.6563 (ptt180) cc_final: 0.6243 (mtp-110) REVERT: G 960 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6558 (pt) REVERT: G 1040 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6413 (ttm-80) REVERT: G 1076 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6539 (p0) REVERT: H 45 LEU cc_start: 0.8708 (mp) cc_final: 0.8199 (tp) REVERT: H 121 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.7416 (mtm-85) REVERT: H 175 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: H 179 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7843 (ttm-80) REVERT: H 233 GLN cc_start: 0.7071 (pp30) cc_final: 0.6553 (pp30) REVERT: I 215 ASP cc_start: 0.7338 (p0) cc_final: 0.7054 (p0) REVERT: J 196 ARG cc_start: 0.7660 (tmt-80) cc_final: 0.7285 (tpt90) REVERT: J 201 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7576 (ttt90) REVERT: J 211 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7552 (ttm110) REVERT: J 294 ARG cc_start: 0.7761 (ptp-110) cc_final: 0.7352 (ptp-170) REVERT: J 304 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7110 (mt0) REVERT: J 409 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6191 (p0) REVERT: J 452 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7004 (mtp) outliers start: 165 outliers final: 114 residues processed: 988 average time/residue: 0.4848 time to fit residues: 760.3662 Evaluate side-chains 976 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 843 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 918 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 LEU Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1040 ARG Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 346 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A1088 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 927 HIS ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN E 74 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G1029 HIS J 396 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126240 restraints weight = 53183.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124778 restraints weight = 29778.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125433 restraints weight = 26395.175| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33972 Z= 0.223 Angle : 0.731 12.320 45964 Z= 0.365 Chirality : 0.044 0.231 5146 Planarity : 0.005 0.070 6034 Dihedral : 7.019 158.514 4640 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.95 % Favored : 93.91 % Rotamer: Outliers : 5.51 % Allowed : 29.06 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4136 helix: 1.37 (0.10), residues: 2412 sheet: -0.93 (0.24), residues: 472 loop : -1.56 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 115 HIS 0.006 0.001 HIS F 791 PHE 0.019 0.002 PHE A 886 TYR 0.026 0.002 TYR F 891 ARG 0.008 0.001 ARG G 192 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 1985) hydrogen bonds : angle 4.67545 ( 5820) covalent geometry : bond 0.00520 (33972) covalent geometry : angle 0.73057 (45964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 843 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 830 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: A 976 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6406 (tp30) REVERT: A 1054 GLU cc_start: 0.8062 (mp0) cc_final: 0.7838 (mt-10) REVERT: B 144 LEU cc_start: 0.7390 (mp) cc_final: 0.6510 (pp) REVERT: B 184 LYS cc_start: 0.7867 (tttt) cc_final: 0.7553 (ttpp) REVERT: B 186 GLN cc_start: 0.7527 (tt0) cc_final: 0.7298 (pt0) REVERT: B 219 GLU cc_start: 0.8070 (pm20) cc_final: 0.7549 (tt0) REVERT: B 237 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7260 (mm-30) REVERT: B 256 ARG cc_start: 0.6965 (ttp80) cc_final: 0.6395 (ptm160) REVERT: B 802 SER cc_start: 0.7663 (m) cc_final: 0.7457 (p) REVERT: B 943 GLU cc_start: 0.6732 (mp0) cc_final: 0.6487 (mp0) REVERT: B 1076 ASN cc_start: 0.6819 (OUTLIER) cc_final: 0.6500 (p0) REVERT: C 233 GLN cc_start: 0.7137 (pp30) cc_final: 0.6648 (pp30) REVERT: E 125 THR cc_start: 0.9029 (p) cc_final: 0.8806 (p) REVERT: E 227 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7816 (mm) REVERT: E 409 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5987 (p0) REVERT: E 452 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7177 (mtp) REVERT: E 461 ILE cc_start: 0.7699 (pt) cc_final: 0.7295 (mp) REVERT: E 478 TRP cc_start: 0.6996 (OUTLIER) cc_final: 0.6748 (m100) REVERT: E 494 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5568 (t0) REVERT: F 56 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8651 (tt) REVERT: F 929 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8332 (mtmm) REVERT: F 931 LEU cc_start: 0.9332 (tp) cc_final: 0.9073 (tp) REVERT: F 976 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6408 (tp30) REVERT: F 1054 GLU cc_start: 0.8089 (mp0) cc_final: 0.7670 (mt-10) REVERT: G 184 LYS cc_start: 0.7973 (tttt) cc_final: 0.7661 (ttpp) REVERT: G 219 GLU cc_start: 0.7918 (pm20) cc_final: 0.7473 (tt0) REVERT: G 237 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7310 (mm-30) REVERT: G 253 GLU cc_start: 0.5198 (mm-30) cc_final: 0.4540 (mm-30) REVERT: G 270 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: G 819 LEU cc_start: 0.6137 (pt) cc_final: 0.5324 (mm) REVERT: G 893 ARG cc_start: 0.6725 (ptt180) cc_final: 0.6336 (mtp-110) REVERT: G 989 LYS cc_start: 0.8536 (mttm) cc_final: 0.8068 (tttt) REVERT: G 990 GLU cc_start: 0.8477 (tp30) cc_final: 0.8217 (tp30) REVERT: G 1040 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6471 (ttm-80) REVERT: G 1076 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6596 (p0) REVERT: H 45 LEU cc_start: 0.8759 (mp) cc_final: 0.8282 (tp) REVERT: H 95 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7765 (mt-10) REVERT: H 146 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6364 (tm-30) REVERT: H 175 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: H 179 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7942 (ttm-80) REVERT: H 220 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7271 (tm-30) REVERT: H 233 GLN cc_start: 0.7124 (pp30) cc_final: 0.6637 (pp30) REVERT: I 215 ASP cc_start: 0.7373 (p0) cc_final: 0.7085 (p0) REVERT: J 177 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: J 200 ARG cc_start: 0.8467 (mmp80) cc_final: 0.8192 (mmm160) REVERT: J 201 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7527 (ttt90) REVERT: J 291 LEU cc_start: 0.8357 (tt) cc_final: 0.8019 (tp) REVERT: J 409 ASP cc_start: 0.6421 (OUTLIER) cc_final: 0.6078 (p0) REVERT: J 452 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7060 (mtp) REVERT: J 465 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6473 (mmm160) outliers start: 196 outliers final: 148 residues processed: 955 average time/residue: 0.4772 time to fit residues: 721.0180 Evaluate side-chains 975 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 807 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1006 CYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 797 LEU Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 826 LEU Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 976 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 807 VAL Chi-restraints excluded: chain G residue 865 HIS Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1027 SER Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1040 ARG Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain J residue 201 ARG Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 0.3980 chunk 153 optimal weight: 0.0870 chunk 289 optimal weight: 2.9990 chunk 141 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 chunk 285 optimal weight: 0.2980 chunk 265 optimal weight: 0.0030 chunk 278 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 overall best weight: 0.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G1029 HIS G1073 GLN J 396 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130929 restraints weight = 52661.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130579 restraints weight = 26644.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131084 restraints weight = 23169.475| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33972 Z= 0.130 Angle : 0.708 12.751 45964 Z= 0.350 Chirality : 0.042 0.243 5146 Planarity : 0.004 0.068 6034 Dihedral : 6.688 169.467 4640 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 3.15 % Allowed : 31.82 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4136 helix: 1.52 (0.11), residues: 2398 sheet: -0.97 (0.23), residues: 488 loop : -1.45 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 128 HIS 0.008 0.001 HIS B1029 PHE 0.020 0.001 PHE G 194 TYR 0.024 0.002 TYR G 187 ARG 0.011 0.001 ARG J 6 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 1985) hydrogen bonds : angle 4.53881 ( 5820) covalent geometry : bond 0.00277 (33972) covalent geometry : angle 0.70752 (45964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 899 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8817 (mm) REVERT: B 17 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7945 (tpp80) REVERT: B 144 LEU cc_start: 0.7679 (mp) cc_final: 0.6941 (pp) REVERT: B 184 LYS cc_start: 0.7943 (tttt) cc_final: 0.7687 (ttpp) REVERT: B 219 GLU cc_start: 0.8023 (pm20) cc_final: 0.7439 (tt0) REVERT: B 237 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7254 (mm-30) REVERT: B 256 ARG cc_start: 0.6935 (ttp80) cc_final: 0.6576 (ptm160) REVERT: B 893 ARG cc_start: 0.6636 (ptt180) cc_final: 0.6156 (mtp-110) REVERT: B 1076 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.6499 (p0) REVERT: C 233 GLN cc_start: 0.6968 (pp30) cc_final: 0.6476 (pp30) REVERT: D 103 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8110 (ptpp) REVERT: E 227 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7863 (mm) REVERT: E 304 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: E 409 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.6124 (p0) REVERT: E 452 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6998 (mtp) REVERT: E 461 ILE cc_start: 0.7691 (pt) cc_final: 0.7314 (mp) REVERT: F 56 LEU cc_start: 0.9002 (tt) cc_final: 0.8711 (tt) REVERT: F 269 TRP cc_start: 0.8765 (t-100) cc_final: 0.8536 (t-100) REVERT: F 931 LEU cc_start: 0.9160 (tp) cc_final: 0.8875 (tp) REVERT: F 1054 GLU cc_start: 0.8017 (mp0) cc_final: 0.7785 (mt-10) REVERT: G 34 ILE cc_start: 0.8704 (mp) cc_final: 0.8446 (mp) REVERT: G 156 TRP cc_start: 0.8127 (m-10) cc_final: 0.7690 (m-90) REVERT: G 219 GLU cc_start: 0.8010 (pm20) cc_final: 0.7474 (tt0) REVERT: G 270 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: G 794 ASN cc_start: 0.8159 (t0) cc_final: 0.7946 (t0) REVERT: G 877 LEU cc_start: 0.8496 (tm) cc_final: 0.7887 (mm) REVERT: G 893 ARG cc_start: 0.6523 (ptt180) cc_final: 0.6238 (mtp-110) REVERT: G 897 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7218 (tptm) REVERT: G 961 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: G 989 LYS cc_start: 0.8306 (mttm) cc_final: 0.7885 (tttt) REVERT: G 1076 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6685 (p0) REVERT: H 45 LEU cc_start: 0.8674 (mp) cc_final: 0.8163 (tp) REVERT: H 175 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: H 179 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: H 215 ASP cc_start: 0.8357 (p0) cc_final: 0.8108 (p0) REVERT: H 220 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7131 (tm-30) REVERT: H 233 GLN cc_start: 0.6945 (pp30) cc_final: 0.6468 (pp30) REVERT: I 215 ASP cc_start: 0.7311 (p0) cc_final: 0.7016 (p0) REVERT: J 96 GLU cc_start: 0.6576 (tm-30) cc_final: 0.6311 (tm-30) REVERT: J 177 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: J 294 ARG cc_start: 0.7596 (ptp-110) cc_final: 0.7182 (ptp-170) REVERT: J 304 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: J 409 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.6101 (p0) REVERT: J 452 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6954 (mtp) outliers start: 112 outliers final: 71 residues processed: 970 average time/residue: 0.4844 time to fit residues: 745.0760 Evaluate side-chains 908 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 823 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1006 CYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 961 GLU Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 409 ASP Chi-restraints excluded: chain J residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 90 optimal weight: 10.0000 chunk 313 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 392 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 180 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1073 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 74 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS G1073 GLN I 126 ASN J 11 ASN ** J 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129035 restraints weight = 53060.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127943 restraints weight = 28431.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128457 restraints weight = 26001.821| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33972 Z= 0.164 Angle : 0.728 12.629 45964 Z= 0.364 Chirality : 0.043 0.329 5146 Planarity : 0.005 0.069 6034 Dihedral : 6.711 170.838 4640 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.71 % Favored : 94.12 % Rotamer: Outliers : 2.81 % Allowed : 32.46 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4136 helix: 1.46 (0.11), residues: 2406 sheet: -1.00 (0.23), residues: 488 loop : -1.46 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 128 HIS 0.008 0.001 HIS B1029 PHE 0.021 0.002 PHE B 844 TYR 0.032 0.002 TYR G 187 ARG 0.015 0.001 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1985) hydrogen bonds : angle 4.65532 ( 5820) covalent geometry : bond 0.00380 (33972) covalent geometry : angle 0.72803 (45964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 838 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 1056 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7153 (tpp80) REVERT: B 17 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7844 (tpp80) REVERT: B 144 LEU cc_start: 0.7628 (mp) cc_final: 0.6994 (pp) REVERT: B 184 LYS cc_start: 0.8020 (tttt) cc_final: 0.7703 (ttpp) REVERT: B 190 ARG cc_start: 0.7887 (tpt-90) cc_final: 0.7451 (mmm160) REVERT: B 219 GLU cc_start: 0.8059 (pm20) cc_final: 0.7458 (tt0) REVERT: B 237 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7300 (mm-30) REVERT: B 256 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6652 (ttm-80) REVERT: B 944 ARG cc_start: 0.6927 (mmt180) cc_final: 0.6709 (mmt180) REVERT: B 989 LYS cc_start: 0.8526 (mttm) cc_final: 0.8006 (tttt) REVERT: B 1076 ASN cc_start: 0.6930 (OUTLIER) cc_final: 0.6635 (p0) REVERT: C 233 GLN cc_start: 0.7076 (pp30) cc_final: 0.6578 (pp30) REVERT: E 134 ARG cc_start: 0.6395 (mtm180) cc_final: 0.5966 (mtm180) REVERT: E 163 ARG cc_start: 0.7097 (mtm110) cc_final: 0.6633 (ptp90) REVERT: E 227 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7763 (mm) REVERT: E 304 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: E 409 ASP cc_start: 0.6369 (OUTLIER) cc_final: 0.6033 (p0) REVERT: E 452 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7123 (mtp) REVERT: E 461 ILE cc_start: 0.7768 (pt) cc_final: 0.7309 (mp) REVERT: F 56 LEU cc_start: 0.9022 (tt) cc_final: 0.8702 (tt) REVERT: F 931 LEU cc_start: 0.9259 (tp) cc_final: 0.8989 (tp) REVERT: F 1054 GLU cc_start: 0.8049 (mp0) cc_final: 0.7807 (mt-10) REVERT: G 156 TRP cc_start: 0.8116 (m-10) cc_final: 0.7662 (m-90) REVERT: G 173 LYS cc_start: 0.5560 (pttm) cc_final: 0.5278 (ptmm) REVERT: G 219 GLU cc_start: 0.8072 (pm20) cc_final: 0.7549 (tt0) REVERT: G 270 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: G 794 ASN cc_start: 0.8178 (t0) cc_final: 0.7941 (t0) REVERT: G 893 ARG cc_start: 0.6612 (ptt180) cc_final: 0.6219 (mtp-110) REVERT: G 989 LYS cc_start: 0.8341 (mttm) cc_final: 0.7920 (tttt) REVERT: G 1076 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6652 (p0) REVERT: H 45 LEU cc_start: 0.8717 (mp) cc_final: 0.8239 (tp) REVERT: H 146 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6203 (tm-30) REVERT: H 175 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: H 179 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7858 (ttm-80) REVERT: H 220 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7193 (tm-30) REVERT: H 233 GLN cc_start: 0.6986 (pp30) cc_final: 0.6515 (pp30) REVERT: I 215 ASP cc_start: 0.7402 (p0) cc_final: 0.7067 (p0) REVERT: J 3 GLU cc_start: 0.6066 (pm20) cc_final: 0.5743 (pm20) REVERT: J 177 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: J 294 ARG cc_start: 0.7678 (ptp-110) cc_final: 0.7257 (ptp-170) REVERT: J 304 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: J 452 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7055 (mtp) outliers start: 100 outliers final: 82 residues processed: 901 average time/residue: 0.4850 time to fit residues: 689.3628 Evaluate side-chains 899 residues out of total 3558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 805 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1092 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1021 ASP Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 409 ASP Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 824 VAL Chi-restraints excluded: chain F residue 891 TYR Chi-restraints excluded: chain F residue 900 VAL Chi-restraints excluded: chain F residue 947 THR Chi-restraints excluded: chain F residue 974 VAL Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 985 SER Chi-restraints excluded: chain G residue 1018 ILE Chi-restraints excluded: chain G residue 1021 ASP Chi-restraints excluded: chain G residue 1039 LEU Chi-restraints excluded: chain G residue 1047 VAL Chi-restraints excluded: chain G residue 1076 ASN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 240 optimal weight: 0.9980 chunk 393 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 337 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 74 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 HIS I 126 ASN J 11 ASN J 74 GLN J 396 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.169029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129135 restraints weight = 53071.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128167 restraints weight = 28496.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128792 restraints weight = 24761.758| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33972 Z= 0.158 Angle : 0.733 12.685 45964 Z= 0.366 Chirality : 0.043 0.336 5146 Planarity : 0.004 0.069 6034 Dihedral : 6.698 177.753 4640 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.29 % Rotamer: Outliers : 3.43 % Allowed : 32.01 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4136 helix: 1.43 (0.11), residues: 2404 sheet: -1.09 (0.23), residues: 498 loop : -1.46 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 128 HIS 0.008 0.001 HIS B1029 PHE 0.020 0.001 PHE F 886 TYR 0.039 0.002 TYR G 187 ARG 0.012 0.001 ARG G 192 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1985) hydrogen bonds : angle 4.66930 ( 5820) covalent geometry : bond 0.00363 (33972) covalent geometry : angle 0.73284 (45964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14512.32 seconds wall clock time: 250 minutes 17.81 seconds (15017.81 seconds total)