Starting phenix.real_space_refine on Fri May 23 07:10:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk2_27481/05_2025/8dk2_27481.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 14634 2.51 5 N 4387 2.21 5 O 4595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3527 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2738 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5720 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 17, 'TRANS': 705} Chain breaks: 2 Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5680 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 17, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "G" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "I" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.80, per 1000 atoms: 0.62 Number of scatterers: 23727 At special positions: 0 Unit cell: (168.67, 145.203, 288.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 58 15.00 Mg 2 11.99 O 4595 8.00 N 4387 7.00 C 14634 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: 5.64 Conformation dependent library (CDL) restraints added in 2.7 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 16 sheets defined 65.9% alpha, 8.5% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.513A pdb=" N SER A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.174A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.844A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.829A pdb=" N SER A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.666A pdb=" N VAL A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.907A pdb=" N VAL A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 272 removed outlier: 4.064A pdb=" N LEU A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.603A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.727A pdb=" N TRP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.517A pdb=" N ARG A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 409 through 425 removed outlier: 4.176A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.170A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.630A pdb=" N ARG B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.553A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.603A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.645A pdb=" N SER B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 220 removed outlier: 4.093A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.806A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.815A pdb=" N LEU B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.534A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.510A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 removed outlier: 3.547A pdb=" N TYR C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.517A pdb=" N LEU C 139 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.014A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.516A pdb=" N PHE C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.872A pdb=" N ILE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.973A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 342 removed outlier: 4.530A pdb=" N LEU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Proline residue: C 264 - end of helix Proline residue: C 290 - end of helix removed outlier: 3.637A pdb=" N ARG C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 741 removed outlier: 3.774A pdb=" N LYS C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.604A pdb=" N ALA C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 808 Processing helix chain 'C' and resid 820 through 848 removed outlier: 4.313A pdb=" N ARG C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix removed outlier: 4.248A pdb=" N GLU C 846 " --> pdb=" O LYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 881 removed outlier: 3.768A pdb=" N VAL C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 880 " --> pdb=" O ASP C 876 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 918 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 947 through 955 Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 985 through 1005 removed outlier: 3.704A pdb=" N LYS C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1010 Processing helix chain 'C' and resid 1028 through 1042 Processing helix chain 'C' and resid 1055 through 1062 Processing helix chain 'C' and resid 1082 through 1087 removed outlier: 3.694A pdb=" N GLU C1087 " --> pdb=" O GLU C1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.570A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.550A pdb=" N ILE D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 341 removed outlier: 4.358A pdb=" N THR D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix removed outlier: 4.121A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 290 - end of helix Processing helix chain 'D' and resid 692 through 741 Processing helix chain 'D' and resid 748 through 757 removed outlier: 3.586A pdb=" N LEU D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 763 No H-bonds generated for 'chain 'D' and resid 761 through 763' Processing helix chain 'D' and resid 764 through 808 Processing helix chain 'D' and resid 820 through 835 removed outlier: 4.220A pdb=" N ARG D 824 " --> pdb=" O VAL D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 848 removed outlier: 4.152A pdb=" N GLU D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 882 removed outlier: 4.303A pdb=" N VAL D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR D 880 " --> pdb=" O ASP D 876 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 882 " --> pdb=" O ASN D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 918 removed outlier: 3.550A pdb=" N ARG D 918 " --> pdb=" O LEU D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 944 removed outlier: 3.718A pdb=" N HIS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 955 Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 985 through 1005 Processing helix chain 'D' and resid 1028 through 1042 removed outlier: 3.672A pdb=" N PHE D1042 " --> pdb=" O ALA D1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1061 removed outlier: 3.784A pdb=" N HIS D1060 " --> pdb=" O ARG D1056 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 130 through 150 removed outlier: 3.705A pdb=" N GLU G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 Proline residue: G 167 - end of helix removed outlier: 3.850A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 195 Processing helix chain 'G' and resid 212 through 218 removed outlier: 4.140A pdb=" N HIS G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 235 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 130 through 150 removed outlier: 4.204A pdb=" N LEU H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 174 removed outlier: 3.646A pdb=" N ILE H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 4.278A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 196 removed outlier: 3.590A pdb=" N HIS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 219 through 236 Processing helix chain 'I' and resid 49 through 63 Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 130 through 150 removed outlier: 3.825A pdb=" N GLU I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 174 Proline residue: I 167 - end of helix removed outlier: 3.831A pdb=" N TYR I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 195 removed outlier: 3.516A pdb=" N GLU I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 218 removed outlier: 4.114A pdb=" N HIS I 216 " --> pdb=" O PRO I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 460 through 472 removed outlier: 7.897A pdb=" N GLU A 463 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N LEU A 482 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ARG A 465 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N PHE A 480 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N PHE A 467 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N TRP A 478 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU A 469 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N GLN A 476 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 29 through 33 removed outlier: 7.232A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 112 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 116 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 124 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1018 through 1021 removed outlier: 3.528A pdb=" N LEU C1020 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C1049 " --> pdb=" O LEU C1020 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 39 " --> pdb=" O PHE C1048 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 890 through 898 removed outlier: 3.754A pdb=" N GLU C 976 " --> pdb=" O VAL C 966 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 968 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 974 " --> pdb=" O ASP C 968 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33 removed outlier: 7.001A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1017 through 1019 removed outlier: 7.025A pdb=" N THR D 39 " --> pdb=" O PHE D1048 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR D1050 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 41 " --> pdb=" O THR D1050 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 40 " --> pdb=" O SER D1064 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D1068 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D1065 " --> pdb=" O LEU D1080 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 890 through 898 removed outlier: 3.980A pdb=" N GLU D 976 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 968 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 974 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.746A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.164A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'I' and resid 159 through 161 1426 hydrogen bonds defined for protein. 4218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 9.69 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8289 1.36 - 1.51: 5987 1.51 - 1.65: 9836 1.65 - 1.80: 49 1.80 - 1.95: 37 Bond restraints: 24198 Sorted by residual: bond pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.32e+00 bond pdb=" CA GLN C 263 " pdb=" C GLN C 263 " ideal model delta sigma weight residual 1.521 1.535 -0.013 1.17e-02 7.31e+03 1.31e+00 bond pdb=" N LEU D 289 " pdb=" CA LEU D 289 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.30e+00 bond pdb=" C LEU D 289 " pdb=" O LEU D 289 " ideal model delta sigma weight residual 1.238 1.251 -0.014 1.28e-02 6.10e+03 1.13e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 32443 1.57 - 3.14: 415 3.14 - 4.71: 53 4.71 - 6.28: 10 6.28 - 7.85: 3 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C ALA C 231 " pdb=" N PHE C 232 " pdb=" CA PHE C 232 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N LEU D 289 " pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 109.81 117.24 -7.43 2.21e+00 2.05e-01 1.13e+01 angle pdb=" N VAL C1073 " pdb=" CA VAL C1073 " pdb=" C VAL C1073 " ideal model delta sigma weight residual 113.20 110.46 2.74 9.60e-01 1.09e+00 8.12e+00 angle pdb=" C SER C 230 " pdb=" N ALA C 231 " pdb=" CA ALA C 231 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.69e+00 angle pdb=" CA LEU D 860 " pdb=" CB LEU D 860 " pdb=" CG LEU D 860 " ideal model delta sigma weight residual 116.30 124.15 -7.85 3.50e+00 8.16e-02 5.02e+00 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 14034 26.56 - 53.12: 625 53.12 - 79.68: 55 79.68 - 106.23: 4 106.23 - 132.79: 1 Dihedral angle restraints: 14719 sinusoidal: 6503 harmonic: 8216 Sorted by residual: dihedral pdb=" O1A AGS C1201 " pdb=" O3A AGS C1201 " pdb=" PA AGS C1201 " pdb=" PB AGS C1201 " ideal model delta sinusoidal sigma weight residual -67.73 65.06 -132.79 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA THR C1050 " pdb=" C THR C1050 " pdb=" N PRO C1051 " pdb=" CA PRO C1051 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN A 18 " pdb=" C GLN A 18 " pdb=" N HIS A 19 " pdb=" CA HIS A 19 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 14716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2397 0.025 - 0.050: 776 0.050 - 0.075: 337 0.075 - 0.101: 132 0.101 - 0.126: 76 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CA ILE D1049 " pdb=" N ILE D1049 " pdb=" C ILE D1049 " pdb=" CB ILE D1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE C1049 " pdb=" N ILE C1049 " pdb=" C ILE C1049 " pdb=" CB ILE C1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL A 485 " pdb=" N VAL A 485 " pdb=" C VAL A 485 " pdb=" CB VAL A 485 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 3715 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 780 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C GLN D 780 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN D 780 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 781 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 783 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LEU D 783 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 783 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 784 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 782 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLN D 782 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN D 782 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 783 " 0.010 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 193 2.57 - 3.15: 19087 3.15 - 3.74: 37455 3.74 - 4.32: 47077 4.32 - 4.90: 77901 Nonbonded interactions: 181713 Sorted by model distance: nonbonded pdb=" NH2 ARG D 78 " pdb="MG MG D1202 " model vdw 1.988 2.250 nonbonded pdb=" N ALA C 69 " pdb="MG MG C1202 " model vdw 2.030 2.250 nonbonded pdb=" NE ARG D 78 " pdb="MG MG D1202 " model vdw 2.047 2.250 nonbonded pdb=" N SER C 70 " pdb="MG MG C1202 " model vdw 2.098 2.250 nonbonded pdb=" O ASN C 67 " pdb="MG MG C1202 " model vdw 2.102 2.170 ... (remaining 181708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 10 through 1083 or resid 1201 through 1202)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'H' selection = (chain 'I' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } 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: 12.980 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: 0.000 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.070 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.002 0.039 24198 Z= 0.123 Angle : 0.466 7.846 32924 Z= 0.256 Chirality : 0.035 0.126 3718 Planarity : 0.004 0.044 4130 Dihedral : 13.702 132.792 9379 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 5.42 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2798 helix: 2.62 (0.13), residues: 1708 sheet: -0.02 (0.33), residues: 279 loop : -0.97 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.003 0.001 HIS D 901 PHE 0.010 0.001 PHE D 187 TYR 0.011 0.001 TYR C 272 ARG 0.002 0.000 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.11744 ( 1478) hydrogen bonds : angle 4.94989 ( 4322) covalent geometry : bond 0.00241 (24198) covalent geometry : angle 0.46600 (32924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 2.637 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: A 60 MET cc_start: 0.8359 (mtp) cc_final: 0.8067 (ttm) REVERT: A 122 MET cc_start: 0.9243 (mtp) cc_final: 0.8740 (mpp) REVERT: A 260 LEU cc_start: 0.9278 (mt) cc_final: 0.8719 (mt) REVERT: A 452 MET cc_start: 0.9133 (mtp) cc_final: 0.8694 (mtt) REVERT: A 484 TYR cc_start: 0.8502 (t80) cc_final: 0.8031 (t80) REVERT: B 25 LEU cc_start: 0.9134 (mt) cc_final: 0.8865 (pp) REVERT: B 122 MET cc_start: 0.9512 (mtp) cc_final: 0.9122 (pmm) REVERT: B 144 ASN cc_start: 0.8270 (t0) cc_final: 0.7827 (t0) REVERT: B 176 LEU cc_start: 0.8383 (mt) cc_final: 0.8041 (tp) REVERT: B 325 HIS cc_start: 0.9065 (m170) cc_final: 0.8814 (t-170) REVERT: C 801 MET cc_start: 0.7573 (tmm) cc_final: 0.7095 (tmm) REVERT: C 901 HIS cc_start: 0.8159 (p-80) cc_final: 0.7805 (p-80) REVERT: C 953 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9361 (tt) REVERT: D 19 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: D 227 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (t70) REVERT: D 1060 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7862 (m170) REVERT: F 74 TYR cc_start: 0.6652 (t80) cc_final: 0.6069 (t80) REVERT: H 95 MET cc_start: 0.1587 (ttp) cc_final: -0.0813 (mmt) outliers start: 69 outliers final: 23 residues processed: 229 average time/residue: 0.3696 time to fit residues: 130.3621 Evaluate side-chains 111 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 163 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 133 GLN B 163 HIS B 240 ASN C 97 GLN C 99 HIS C 103 GLN C 258 GLN C 276 GLN C 329 GLN C 336 HIS C 775 HIS C 858 GLN C1060 HIS D 312 HIS D 712 GLN D 726 GLN F 57 GLN G 57 GLN G 80 ASN G 110 GLN G 116 GLN G 127 GLN G 149 GLN G 157 GLN G 196 HIS G 216 HIS H 57 GLN H 69 HIS H 205 HIS I 57 GLN I 80 ASN I 110 GLN I 127 GLN I 142 GLN I 149 GLN I 157 GLN I 168 GLN I 224 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.075008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049243 restraints weight = 186656.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.048818 restraints weight = 109526.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048813 restraints weight = 74572.594| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24198 Z= 0.183 Angle : 0.593 8.413 32924 Z= 0.312 Chirality : 0.039 0.151 3718 Planarity : 0.004 0.066 4130 Dihedral : 13.294 141.754 3808 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.17 % Allowed : 2.42 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2798 helix: 2.61 (0.12), residues: 1729 sheet: -0.05 (0.32), residues: 272 loop : -1.13 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 290 HIS 0.013 0.001 HIS D 775 PHE 0.051 0.002 PHE D 844 TYR 0.026 0.002 TYR D 995 ARG 0.010 0.000 ARG F 109 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 1478) hydrogen bonds : angle 4.06706 ( 4322) covalent geometry : bond 0.00394 (24198) covalent geometry : angle 0.59327 (32924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9262 (mtp) cc_final: 0.8656 (mpp) REVERT: B 25 LEU cc_start: 0.9162 (mt) cc_final: 0.8887 (pp) REVERT: B 122 MET cc_start: 0.9580 (mtp) cc_final: 0.9048 (pmm) REVERT: B 176 LEU cc_start: 0.8568 (mt) cc_final: 0.8206 (tp) REVERT: B 288 LEU cc_start: 0.8336 (tt) cc_final: 0.8115 (pp) REVERT: B 317 MET cc_start: 0.8757 (mpp) cc_final: 0.8443 (mtm) REVERT: B 325 HIS cc_start: 0.9095 (m170) cc_final: 0.8841 (t70) REVERT: C 901 HIS cc_start: 0.8256 (p-80) cc_final: 0.7899 (p-80) REVERT: D 171 MET cc_start: 0.9086 (mtp) cc_final: 0.8863 (mtp) REVERT: F 74 TYR cc_start: 0.6463 (t80) cc_final: 0.6051 (t80) REVERT: H 95 MET cc_start: 0.1659 (ttp) cc_final: -0.0419 (mmt) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.4101 time to fit residues: 65.7009 Evaluate side-chains 75 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 253 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS C 258 GLN C 858 GLN D 312 HIS F 69 HIS G 205 HIS H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.075269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049110 restraints weight = 186139.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049076 restraints weight = 108276.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048793 restraints weight = 73659.735| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24198 Z= 0.140 Angle : 0.524 8.842 32924 Z= 0.275 Chirality : 0.038 0.269 3718 Planarity : 0.004 0.042 4130 Dihedral : 13.296 134.288 3808 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.16), residues: 2798 helix: 2.78 (0.12), residues: 1728 sheet: 0.08 (0.33), residues: 272 loop : -1.08 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 128 HIS 0.012 0.001 HIS A 163 PHE 0.030 0.002 PHE D 844 TYR 0.016 0.001 TYR C 928 ARG 0.005 0.000 ARG D1059 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1478) hydrogen bonds : angle 3.87509 ( 4322) covalent geometry : bond 0.00299 (24198) covalent geometry : angle 0.52361 (32924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9232 (mtp) cc_final: 0.8378 (mmp) REVERT: A 452 MET cc_start: 0.8781 (mtm) cc_final: 0.8485 (ptp) REVERT: B 25 LEU cc_start: 0.9114 (mt) cc_final: 0.8842 (pp) REVERT: B 122 MET cc_start: 0.9554 (mtp) cc_final: 0.9028 (pmm) REVERT: B 144 ASN cc_start: 0.8616 (t0) cc_final: 0.8344 (t0) REVERT: B 176 LEU cc_start: 0.8477 (mt) cc_final: 0.8048 (tp) REVERT: B 317 MET cc_start: 0.8758 (mpp) cc_final: 0.8443 (mtm) REVERT: B 325 HIS cc_start: 0.9095 (m170) cc_final: 0.8882 (t70) REVERT: C 171 MET cc_start: 0.8448 (mtp) cc_final: 0.8097 (ttt) REVERT: C 901 HIS cc_start: 0.8284 (p-80) cc_final: 0.7933 (p-80) REVERT: D 801 MET cc_start: 0.7841 (mmm) cc_final: 0.7561 (mmt) REVERT: F 74 TYR cc_start: 0.6107 (t80) cc_final: 0.5721 (t80) REVERT: H 95 MET cc_start: 0.1678 (ttp) cc_final: 0.0309 (ttm) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.3639 time to fit residues: 54.9728 Evaluate side-chains 68 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 238 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 204 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 248 optimal weight: 0.0040 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 858 GLN D 775 HIS H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050065 restraints weight = 186855.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049376 restraints weight = 120943.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049175 restraints weight = 87675.953| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.114 Angle : 0.494 8.766 32924 Z= 0.260 Chirality : 0.037 0.138 3718 Planarity : 0.003 0.038 4130 Dihedral : 13.301 131.442 3808 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2798 helix: 2.88 (0.12), residues: 1732 sheet: 0.17 (0.33), residues: 271 loop : -1.06 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 128 HIS 0.008 0.001 HIS A 163 PHE 0.022 0.001 PHE D 844 TYR 0.012 0.001 TYR C 928 ARG 0.006 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1478) hydrogen bonds : angle 3.75498 ( 4322) covalent geometry : bond 0.00235 (24198) covalent geometry : angle 0.49399 (32924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9142 (mtp) cc_final: 0.8778 (mpp) REVERT: A 452 MET cc_start: 0.8830 (mtm) cc_final: 0.8584 (mtp) REVERT: B 25 LEU cc_start: 0.9105 (mt) cc_final: 0.8846 (pp) REVERT: B 122 MET cc_start: 0.9600 (mtp) cc_final: 0.9062 (pmm) REVERT: B 144 ASN cc_start: 0.8435 (t0) cc_final: 0.8131 (t0) REVERT: B 176 LEU cc_start: 0.8378 (mt) cc_final: 0.7995 (tp) REVERT: B 325 HIS cc_start: 0.9040 (m170) cc_final: 0.8602 (t70) REVERT: C 171 MET cc_start: 0.8441 (mtp) cc_final: 0.8072 (ttt) REVERT: C 801 MET cc_start: 0.7272 (tpp) cc_final: 0.6976 (tpp) REVERT: C 901 HIS cc_start: 0.8309 (p-80) cc_final: 0.7980 (p-80) REVERT: D 171 MET cc_start: 0.8957 (mtp) cc_final: 0.8722 (mtp) REVERT: D 801 MET cc_start: 0.7626 (mmm) cc_final: 0.7278 (mmt) REVERT: F 74 TYR cc_start: 0.5983 (t80) cc_final: 0.5617 (t80) REVERT: H 95 MET cc_start: 0.2123 (ttp) cc_final: 0.0903 (ttm) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.3595 time to fit residues: 52.4479 Evaluate side-chains 72 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 159 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 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 19 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 HIS C 858 GLN C 947 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.075808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051853 restraints weight = 186416.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049729 restraints weight = 136016.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049828 restraints weight = 87449.243| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24198 Z= 0.106 Angle : 0.471 8.930 32924 Z= 0.251 Chirality : 0.036 0.135 3718 Planarity : 0.003 0.044 4130 Dihedral : 13.303 127.776 3808 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.04 % Allowed : 0.92 % Favored : 99.04 % 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: 2.47 (0.17), residues: 2798 helix: 2.98 (0.12), residues: 1725 sheet: 0.26 (0.33), residues: 275 loop : -1.00 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 128 HIS 0.006 0.001 HIS A 163 PHE 0.021 0.001 PHE C 242 TYR 0.011 0.001 TYR C 928 ARG 0.003 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1478) hydrogen bonds : angle 3.64388 ( 4322) covalent geometry : bond 0.00213 (24198) covalent geometry : angle 0.47133 (32924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9170 (mtp) cc_final: 0.8829 (mpp) REVERT: A 185 MET cc_start: 0.8801 (mtm) cc_final: 0.8375 (mtm) REVERT: A 452 MET cc_start: 0.8757 (mtm) cc_final: 0.8515 (mtp) REVERT: B 25 LEU cc_start: 0.9004 (mt) cc_final: 0.8796 (pp) REVERT: B 122 MET cc_start: 0.9536 (mtp) cc_final: 0.9052 (pmm) REVERT: B 144 ASN cc_start: 0.8649 (t0) cc_final: 0.8276 (t0) REVERT: B 176 LEU cc_start: 0.8564 (mt) cc_final: 0.8108 (tp) REVERT: B 325 HIS cc_start: 0.8985 (m170) cc_final: 0.8678 (t70) REVERT: C 171 MET cc_start: 0.8379 (mtp) cc_final: 0.7990 (ttt) REVERT: C 801 MET cc_start: 0.7657 (tpp) cc_final: 0.7302 (tpp) REVERT: C 901 HIS cc_start: 0.8374 (p-80) cc_final: 0.7936 (p-80) REVERT: D 171 MET cc_start: 0.8953 (mtp) cc_final: 0.8713 (mtp) REVERT: D 801 MET cc_start: 0.7772 (mmm) cc_final: 0.7505 (mmt) REVERT: F 74 TYR cc_start: 0.6131 (t80) cc_final: 0.5751 (t80) REVERT: H 95 MET cc_start: 0.1604 (ttp) cc_final: 0.0206 (mtm) REVERT: I 59 MET cc_start: 0.4628 (tpt) cc_final: 0.4034 (tpt) REVERT: I 143 HIS cc_start: 0.8886 (m-70) cc_final: 0.8682 (m-70) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.3720 time to fit residues: 55.1125 Evaluate side-chains 70 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.075443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050765 restraints weight = 185487.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049972 restraints weight = 108836.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049375 restraints weight = 81290.159| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.113 Angle : 0.476 8.541 32924 Z= 0.251 Chirality : 0.036 0.133 3718 Planarity : 0.003 0.051 4130 Dihedral : 13.278 123.761 3808 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 0.83 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.17), residues: 2798 helix: 3.02 (0.12), residues: 1726 sheet: 0.29 (0.33), residues: 273 loop : -1.04 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 292 HIS 0.006 0.001 HIS A 163 PHE 0.021 0.001 PHE C 242 TYR 0.009 0.001 TYR C 891 ARG 0.012 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 1478) hydrogen bonds : angle 3.62717 ( 4322) covalent geometry : bond 0.00234 (24198) covalent geometry : angle 0.47606 (32924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9190 (mtp) cc_final: 0.8597 (mpp) REVERT: A 452 MET cc_start: 0.8757 (mtm) cc_final: 0.8540 (mtp) REVERT: A 484 TYR cc_start: 0.8545 (t80) cc_final: 0.8293 (t80) REVERT: B 25 LEU cc_start: 0.9034 (mt) cc_final: 0.8816 (pp) REVERT: B 122 MET cc_start: 0.9529 (mtp) cc_final: 0.9057 (pmm) REVERT: B 144 ASN cc_start: 0.8548 (t0) cc_final: 0.8172 (t0) REVERT: B 176 LEU cc_start: 0.8538 (mt) cc_final: 0.8107 (tp) REVERT: B 325 HIS cc_start: 0.9043 (m170) cc_final: 0.8680 (t70) REVERT: C 171 MET cc_start: 0.8330 (mtp) cc_final: 0.7929 (ttt) REVERT: C 801 MET cc_start: 0.7573 (tpp) cc_final: 0.7191 (tpp) REVERT: C 901 HIS cc_start: 0.8399 (p-80) cc_final: 0.7951 (p-80) REVERT: D 801 MET cc_start: 0.7720 (mmm) cc_final: 0.7363 (mmt) REVERT: F 74 TYR cc_start: 0.6061 (t80) cc_final: 0.5689 (t80) REVERT: H 95 MET cc_start: 0.2609 (ttp) cc_final: 0.1429 (mtm) REVERT: I 59 MET cc_start: 0.5375 (tpt) cc_final: 0.4592 (tpt) REVERT: I 143 HIS cc_start: 0.8999 (m-70) cc_final: 0.8764 (m-70) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.3715 time to fit residues: 51.8134 Evaluate side-chains 69 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 24 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 246 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 858 GLN D1022 GLN H 205 HIS H 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.074807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050482 restraints weight = 187642.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048355 restraints weight = 124405.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.048681 restraints weight = 88432.472| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24198 Z= 0.158 Angle : 0.517 8.221 32924 Z= 0.273 Chirality : 0.037 0.137 3718 Planarity : 0.004 0.040 4130 Dihedral : 13.254 121.749 3808 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 0.04 % Allowed : 1.13 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.16), residues: 2798 helix: 2.98 (0.12), residues: 1728 sheet: 0.20 (0.33), residues: 278 loop : -1.09 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 23 HIS 0.005 0.001 HIS G 143 PHE 0.019 0.002 PHE C 242 TYR 0.012 0.001 TYR C 862 ARG 0.007 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1478) hydrogen bonds : angle 3.74258 ( 4322) covalent geometry : bond 0.00337 (24198) covalent geometry : angle 0.51656 (32924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8349 (ttm) cc_final: 0.7969 (ttp) REVERT: A 122 MET cc_start: 0.9225 (mtp) cc_final: 0.8631 (mpp) REVERT: A 231 LEU cc_start: 0.8470 (tp) cc_final: 0.8110 (pp) REVERT: A 452 MET cc_start: 0.8785 (mtm) cc_final: 0.8476 (mtp) REVERT: A 484 TYR cc_start: 0.8540 (t80) cc_final: 0.8281 (t80) REVERT: B 122 MET cc_start: 0.9500 (mtp) cc_final: 0.9060 (pmm) REVERT: B 144 ASN cc_start: 0.8677 (t0) cc_final: 0.8267 (t0) REVERT: B 176 LEU cc_start: 0.8725 (mt) cc_final: 0.8254 (tp) REVERT: B 325 HIS cc_start: 0.9008 (m170) cc_final: 0.8770 (t70) REVERT: C 171 MET cc_start: 0.8375 (mtp) cc_final: 0.7965 (ttt) REVERT: C 801 MET cc_start: 0.7767 (tpp) cc_final: 0.7512 (tpp) REVERT: C 901 HIS cc_start: 0.8368 (p-80) cc_final: 0.7836 (p-80) REVERT: D 801 MET cc_start: 0.7795 (mmm) cc_final: 0.7482 (mmt) REVERT: F 74 TYR cc_start: 0.6068 (t80) cc_final: 0.5695 (t80) REVERT: H 95 MET cc_start: 0.2355 (ttp) cc_final: 0.1077 (mtm) REVERT: I 143 HIS cc_start: 0.9033 (m-70) cc_final: 0.8783 (m-70) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.3740 time to fit residues: 52.2915 Evaluate side-chains 69 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 156 optimal weight: 2.9990 chunk 269 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049705 restraints weight = 186228.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049322 restraints weight = 121606.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049046 restraints weight = 85089.928| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24198 Z= 0.117 Angle : 0.489 9.006 32924 Z= 0.258 Chirality : 0.037 0.139 3718 Planarity : 0.003 0.040 4130 Dihedral : 13.183 119.352 3808 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 0.75 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2798 helix: 3.00 (0.12), residues: 1729 sheet: 0.25 (0.33), residues: 278 loop : -1.09 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 128 HIS 0.007 0.001 HIS G 143 PHE 0.020 0.001 PHE C 242 TYR 0.009 0.001 TYR C 862 ARG 0.007 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 1478) hydrogen bonds : angle 3.65957 ( 4322) covalent geometry : bond 0.00245 (24198) covalent geometry : angle 0.48917 (32924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8443 (ttm) cc_final: 0.8074 (ttp) REVERT: A 122 MET cc_start: 0.9218 (mtp) cc_final: 0.8681 (mpp) REVERT: A 452 MET cc_start: 0.8781 (mtm) cc_final: 0.8501 (mtp) REVERT: A 484 TYR cc_start: 0.8553 (t80) cc_final: 0.8313 (t80) REVERT: B 122 MET cc_start: 0.9555 (mtp) cc_final: 0.9066 (pmm) REVERT: B 144 ASN cc_start: 0.8470 (t0) cc_final: 0.8087 (t0) REVERT: B 176 LEU cc_start: 0.8581 (mt) cc_final: 0.8160 (tp) REVERT: B 325 HIS cc_start: 0.9069 (m170) cc_final: 0.8755 (t70) REVERT: C 801 MET cc_start: 0.7804 (tpp) cc_final: 0.7412 (tpp) REVERT: C 901 HIS cc_start: 0.8405 (p-80) cc_final: 0.7871 (p-80) REVERT: D 801 MET cc_start: 0.7662 (mmm) cc_final: 0.7326 (mmt) REVERT: F 74 TYR cc_start: 0.5991 (t80) cc_final: 0.5628 (t80) REVERT: H 95 MET cc_start: 0.3005 (ttp) cc_final: 0.1984 (mtm) REVERT: I 59 MET cc_start: 0.5406 (tpt) cc_final: 0.4559 (tpt) REVERT: I 143 HIS cc_start: 0.9014 (m-70) cc_final: 0.8781 (m-70) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3583 time to fit residues: 51.1528 Evaluate side-chains 69 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 1 optimal weight: 0.6980 chunk 157 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.075060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049402 restraints weight = 186389.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048269 restraints weight = 130743.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.048997 restraints weight = 87086.728| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24198 Z= 0.135 Angle : 0.501 8.889 32924 Z= 0.265 Chirality : 0.037 0.138 3718 Planarity : 0.003 0.040 4130 Dihedral : 13.154 118.870 3808 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.17), residues: 2798 helix: 3.02 (0.12), residues: 1725 sheet: 0.22 (0.33), residues: 278 loop : -1.05 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 23 HIS 0.007 0.001 HIS G 143 PHE 0.018 0.001 PHE C 242 TYR 0.009 0.001 TYR D 83 ARG 0.006 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1478) hydrogen bonds : angle 3.68434 ( 4322) covalent geometry : bond 0.00289 (24198) covalent geometry : angle 0.50130 (32924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9099 (m-10) cc_final: 0.8836 (m-10) REVERT: A 122 MET cc_start: 0.9268 (mtp) cc_final: 0.8606 (mpp) REVERT: A 452 MET cc_start: 0.8831 (mtm) cc_final: 0.8475 (mtp) REVERT: A 484 TYR cc_start: 0.8576 (t80) cc_final: 0.8319 (t80) REVERT: B 122 MET cc_start: 0.9549 (mtp) cc_final: 0.9072 (pmm) REVERT: B 144 ASN cc_start: 0.8547 (t0) cc_final: 0.8119 (t0) REVERT: B 317 MET cc_start: 0.8820 (mtm) cc_final: 0.8563 (ptt) REVERT: B 325 HIS cc_start: 0.9068 (m170) cc_final: 0.8709 (t70) REVERT: C 801 MET cc_start: 0.7867 (tpp) cc_final: 0.7619 (tpp) REVERT: C 901 HIS cc_start: 0.8461 (p-80) cc_final: 0.7938 (p-80) REVERT: D 801 MET cc_start: 0.7651 (mmm) cc_final: 0.7324 (mmt) REVERT: F 74 TYR cc_start: 0.5939 (t80) cc_final: 0.5587 (t80) REVERT: H 95 MET cc_start: 0.2807 (ttp) cc_final: 0.1935 (mtm) REVERT: I 59 MET cc_start: 0.5364 (tpt) cc_final: 0.4511 (tpt) REVERT: I 143 HIS cc_start: 0.9031 (m-70) cc_final: 0.8796 (m-70) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3608 time to fit residues: 49.3070 Evaluate side-chains 66 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 56 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.074892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049336 restraints weight = 188027.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048187 restraints weight = 128501.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048742 restraints weight = 88919.352| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24198 Z= 0.149 Angle : 0.514 8.950 32924 Z= 0.273 Chirality : 0.037 0.139 3718 Planarity : 0.003 0.039 4130 Dihedral : 13.148 118.873 3808 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2798 helix: 2.96 (0.12), residues: 1735 sheet: 0.14 (0.33), residues: 278 loop : -1.19 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 23 HIS 0.007 0.001 HIS G 143 PHE 0.018 0.002 PHE C 242 TYR 0.014 0.001 TYR C 83 ARG 0.006 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1478) hydrogen bonds : angle 3.73310 ( 4322) covalent geometry : bond 0.00321 (24198) covalent geometry : angle 0.51404 (32924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8266 (ttm) cc_final: 0.7966 (ttp) REVERT: A 122 MET cc_start: 0.9237 (mtp) cc_final: 0.8568 (mpp) REVERT: A 452 MET cc_start: 0.8846 (mtm) cc_final: 0.8491 (mtp) REVERT: A 484 TYR cc_start: 0.8624 (t80) cc_final: 0.8342 (t80) REVERT: B 122 MET cc_start: 0.9580 (mtp) cc_final: 0.9133 (pmm) REVERT: B 144 ASN cc_start: 0.8604 (t0) cc_final: 0.8252 (t0) REVERT: B 325 HIS cc_start: 0.9091 (m170) cc_final: 0.8681 (t70) REVERT: C 801 MET cc_start: 0.7909 (tpp) cc_final: 0.7647 (tpp) REVERT: C 901 HIS cc_start: 0.8480 (p-80) cc_final: 0.7940 (p-80) REVERT: D 801 MET cc_start: 0.7654 (mmm) cc_final: 0.7329 (mmt) REVERT: F 74 TYR cc_start: 0.5860 (t80) cc_final: 0.5509 (t80) REVERT: H 95 MET cc_start: 0.3991 (ttp) cc_final: 0.2824 (mtm) REVERT: I 59 MET cc_start: 0.5405 (tpt) cc_final: 0.4565 (tpt) REVERT: I 143 HIS cc_start: 0.8926 (m-70) cc_final: 0.8657 (m-70) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3484 time to fit residues: 44.8401 Evaluate side-chains 66 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 65 optimal weight: 8.9990 chunk 243 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.074077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048379 restraints weight = 188127.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047339 restraints weight = 122954.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.048012 restraints weight = 87483.577| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24198 Z= 0.209 Angle : 0.590 8.690 32924 Z= 0.312 Chirality : 0.039 0.152 3718 Planarity : 0.004 0.049 4130 Dihedral : 13.193 119.876 3808 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.16), residues: 2798 helix: 2.73 (0.12), residues: 1734 sheet: 0.13 (0.33), residues: 272 loop : -1.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 23 HIS 0.008 0.001 HIS D1069 PHE 0.020 0.002 PHE B 336 TYR 0.022 0.002 TYR G 62 ARG 0.006 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 1478) hydrogen bonds : angle 3.96938 ( 4322) covalent geometry : bond 0.00456 (24198) covalent geometry : angle 0.59012 (32924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8888.21 seconds wall clock time: 155 minutes 43.80 seconds (9343.80 seconds total)